{ "type": "genome", "identifier": "GCF_014857905.1", "organism": "Agilicoccus flavus", "title": "Agilicoccus flavus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "sun-yat sen university", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014857905.1", "bioproject": "PRJNA224116", "biosample": "SAMN16088028", "wgs_master": "JACYXE000000000.1", "refseq_category": "reference genome", "taxid": "2775968", "species_taxid": "2775968", "organism_name": "Agilicoccus flavus", "infraspecific_name": "strain=SYSU M44304", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/10/06", "asm_name": "ASM1485790v1", "asm_submitter": "sun-yat sen university", "gbrs_paired_asm": "GCA_014857905.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/857/905/GCF_014857905.1_ASM1485790v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4234396", "genome_size_ungapped": "4234396", "gc_percent": "73.500000", "replicon_count": "0", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014857905.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "3817", "protein_coding_gene_count": "3683", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-10-06", "dateModified": "2020-10-06", "datePublished": "2020-10-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Agilicoccus flavus" ], "sample_taxid": [ "2775968" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Pearl River" ], "sample_host_location_id": [], "data_size": "1.114 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4234396", "Number of Sequences": "35", "Longest Sequences (bp)": "795713", "N50 (bp)": "256623", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.5", "Number of CDSs": "3801", "Average Protein Length": "330.2", "Coding Ratio (%)": "88.9", "Number of rRNAs": "1", "Number of tRNAs": "57", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mobilicoccus pelagius", "strain": "strain=NBRC 104925", "accession": "GCA_000247995.2", "taxid": 746032, "species_taxid": 746032, "relation_to_type": "type", "validated": true, "ani": 79.3546, "matched_fragments": 580, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mobilicoccus massiliensis", "strain": "strain=SIT2", "accession": "GCA_000826525.2", "taxid": 1522310, "species_taxid": 1522310, "relation_to_type": "type", "validated": true, "ani": 79.2954, "matched_fragments": 577, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineosphaera limosa", "strain": "strain=DSM 14548", "accession": "GCA_013409325.1", "taxid": 111564, "species_taxid": 111564, "relation_to_type": "type", "validated": true, "ani": 79.1385, "matched_fragments": 640, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arsenicicoccus bolidensis", "strain": "strain=DSM 15745", "accession": "GCA_000426385.1", "taxid": 229480, "species_taxid": 229480, "relation_to_type": "type", "validated": true, "ani": 78.8679, "matched_fragments": 484, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arsenicicoccus cauae", "strain": "strain=MKL-02", "accession": "GCA_009707125.1", "taxid": 2663847, "species_taxid": 2663847, "relation_to_type": "type", "validated": true, "ani": 78.6814, "matched_fragments": 459, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Knoellia flava", "strain": "strain=CGMCC 1.10749", "accession": "GCA_014636255.1", "taxid": 913969, "species_taxid": 913969, "relation_to_type": "type", "validated": true, "ani": 78.666, "matched_fragments": 486, "total_fragments": 1396, "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": 78.6617, "matched_fragments": 550, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Knoellia remsis", "strain": "strain=ATCC BAA-1496", "accession": "GCA_003002895.1", "taxid": 407159, "species_taxid": 407159, "relation_to_type": "type", "validated": true, "ani": 78.619, "matched_fragments": 463, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter endophyticus", "strain": "strain=YIM B02568", "accession": "GCA_016888335.1", "taxid": 2806261, "species_taxid": 2806261, "relation_to_type": "type", "validated": true, "ani": 78.6007, "matched_fragments": 418, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Knoellia flava", "strain": "strain=TL1", "accession": "GCA_000768675.1", "taxid": 913969, "species_taxid": 913969, "relation_to_type": "type", "validated": true, "ani": 78.5611, "matched_fragments": 492, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Knoellia subterranea", "strain": "strain=KCTC 19937", "accession": "GCA_000768685.1", "taxid": 184882, "species_taxid": 184882, "relation_to_type": "type", "validated": true, "ani": 78.3, "matched_fragments": 390, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter melonis", "strain": "strain=NBRC107855", "accession": "GCA_020567375.1", "taxid": 262209, "species_taxid": 262209, "relation_to_type": "type", "validated": true, "ani": 78.2527, "matched_fragments": 522, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter indicus", "strain": "strain=CGMCC 1.12511", "accession": "GCA_900176385.1", "taxid": 857417, "species_taxid": 857417, "relation_to_type": "type", "validated": true, "ani": 78.2407, "matched_fragments": 448, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter anophelis", "strain": "strain=NBRC 107843", "accession": "GCA_001570945.1", "taxid": 319054, "species_taxid": 319054, "relation_to_type": "type", "validated": true, "ani": 78.2101, "matched_fragments": 421, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter terrae", "strain": "strain=NBRC 107853", "accession": "GCA_001591405.1", "taxid": 103817, "species_taxid": 103817, "relation_to_type": "type", "validated": true, "ani": 78.1764, "matched_fragments": 463, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phycicoccus endophyticus", "strain": "strain=IP6SC6", "accession": "GCA_011326735.1", "taxid": 1690220, "species_taxid": 1690220, "relation_to_type": "type", "validated": true, "ani": 78.1298, "matched_fragments": 467, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phycicoccus endophyticus", "strain": "strain=CGMCC 4.7300", "accession": "GCA_014646175.1", "taxid": 1690220, "species_taxid": 1690220, "relation_to_type": "type", "validated": true, "ani": 78.0884, "matched_fragments": 478, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Intrasporangium chromatireducens", "strain": "strain=Q5-1", "accession": "GCA_000576575.1", "taxid": 1386088, "species_taxid": 1386088, "relation_to_type": "type", "validated": true, "ani": 78.0509, "matched_fragments": 402, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phycicoccus flavus", "strain": "strain=CMS6Z-2", "accession": "GCA_004025965.2", "taxid": 2502783, "species_taxid": 2502783, "relation_to_type": "type", "validated": true, "ani": 77.9951, "matched_fragments": 553, "total_fragments": 1396, "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": 77.6828, "matched_fragments": 357, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flexivirga aerilata", "strain": "strain=ID2601S", "accession": "GCA_013002715.1", "taxid": 1656889, "species_taxid": 1656889, "relation_to_type": "type", "validated": true, "ani": 77.594, "matched_fragments": 415, "total_fragments": 1396, "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": 76.9414, "matched_fragments": 410, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas timonensis", "strain": "strain=SN7", "accession": "GCA_900046455.1", "taxid": 1689271, "species_taxid": 1689271, "relation_to_type": "type", "validated": true, "ani": 76.7885, "matched_fragments": 339, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sediminihabitans luteus", "strain": "strain=NBRC 108568", "accession": "GCA_016863455.1", "taxid": 1138585, "species_taxid": 1138585, "relation_to_type": "type", "validated": true, "ani": 76.7357, "matched_fragments": 400, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sediminihabitans luteus", "strain": "strain=DSM 25478", "accession": "GCA_002797595.1", "taxid": 1138585, "species_taxid": 1138585, "relation_to_type": "type", "validated": true, "ani": 76.7127, "matched_fragments": 402, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineococcus xinjiangensis", "strain": "strain=DSM 22857", "accession": "GCA_002934625.1", "taxid": 512762, "species_taxid": 512762, "relation_to_type": "type", "validated": true, "ani": 76.6424, "matched_fragments": 406, "total_fragments": 1396, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_014857905.1", "gtdb_species": "s__JACYXE01 sp014857905", "ani": 100.0, "matched_fragments": 1394, "total_fragments": 1396, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JACYXE01", "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_001515525.1", "gtdb_species": "s__Piscicoccus intestinalis", "ani": 79.8043, "matched_fragments": 646, "total_fragments": 1396, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Piscicoccus", "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_000247995.1", "gtdb_species": "s__Mobilicoccus pelagius", "ani": 79.3145, "matched_fragments": 585, "total_fragments": 1396, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Mobilicoccus", "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_000826525.2", "gtdb_species": "s__Mobilicoccus massiliensis", "ani": 79.2837, "matched_fragments": 577, "total_fragments": 1396, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Mobilicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": 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