{ "type": "genome", "identifier": "GCF_000348785.1", "organism": "Ilumatobacter coccineus YM16-304", "title": "Ilumatobacter coccineus YM16-304", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000348785.1", "bioproject": "PRJNA224116", "biosample": "SAMD00060985", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1313172", "species_taxid": "467094", "organism_name": "Ilumatobacter coccineus YM16-304", "infraspecific_name": "strain=YM16-304", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/03/15", "asm_name": "ASM34878v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_000348785.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/348/785/GCF_000348785.1_ASM34878v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4830181", "genome_size_ungapped": "4830181", "gc_percent": "67.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000348785.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "4306", "protein_coding_gene_count": "4235", "non_coding_gene_count": "55", "pubmed_id": "23524358" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-03-15", "dateModified": "2013-03-15", "datePublished": "2013-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Ilumatobacter coccineus YM16-304" ], "sample_taxid": [ "1313172" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.291 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)": "4830181", "Number of Sequences": "1", "Longest Sequences (bp)": "4830181", "N50 (bp)": "4830181", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.3", "Number of CDSs": "4277", "Average Protein Length": "347.8", "Coding Ratio (%)": "92.4", "Number of rRNAs": "6", "Number of tRNAs": "52", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ilumatobacter coccineus", "strain": "strain=YM16-304", "accession": "GCA_000348785.1", "taxid": 467094, "species_taxid": 467094, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1608, "total_fragments": 1610, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Ilumatobacter nonamiensis", "strain": "strain=YM16-303", "accession": "GCA_000350145.1", "taxid": 467093, "species_taxid": 467093, "relation_to_type": "type", "validated": true, "ani": 79.6642, "matched_fragments": 641, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ilumatobacter fluminis", "strain": "strain=DSM 18936", "accession": "GCA_004364865.1", "taxid": 467091, "species_taxid": 467091, "relation_to_type": "type", "validated": true, "ani": 77.7832, "matched_fragments": 552, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desertimonas flava", "strain": "strain=SYSU D60003", "accession": "GCA_003426815.1", "taxid": 2064846, "species_taxid": 2064846, "relation_to_type": "type", "validated": true, "ani": 77.1313, "matched_fragments": 481, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomarinicola tropica", "strain": "strain=SCSIO 58843", "accession": "GCA_009650215.1", "taxid": 2789776, "species_taxid": 2789776, "relation_to_type": "type", "validated": true, "ani": 76.5411, "matched_fragments": 273, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhabdothermincola salaria", "strain": "strain=EGI L10124", "accession": "GCA_021246445.1", "taxid": 2903142, "species_taxid": 2903142, "relation_to_type": "type", "validated": true, "ani": 76.5026, "matched_fragments": 245, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Euzebya tangerina", "strain": "strain=F10", "accession": "GCA_003074135.1", "taxid": 591198, "species_taxid": 591198, "relation_to_type": "type", "validated": true, "ani": 75.4612, "matched_fragments": 97, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces indiaensis", "strain": "strain=DSM 43803", "accession": "GCA_021474405.1", "taxid": 284033, "species_taxid": 284033, "relation_to_type": "type", "validated": true, "ani": 75.4328, "matched_fragments": 155, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces angustmyceticus", "strain": "strain=JCM 4053", "accession": "GCA_019933235.1", "taxid": 285578, "species_taxid": 285578, "relation_to_type": "type", "validated": true, "ani": 75.3729, "matched_fragments": 190, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces lomondensis", "strain": "strain=DSM 41428", "accession": "GCA_021440105.1", "taxid": 68229, "species_taxid": 68229, "relation_to_type": "type", "validated": true, "ani": 75.2218, "matched_fragments": 197, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blastococcus xanthinilyticus", "strain": "strain=DSM 46842", "accession": "GCA_008124835.1", "taxid": 1564164, "species_taxid": 1564164, "relation_to_type": "type", "validated": true, "ani": 75.2203, "matched_fragments": 174, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geodermatophilus siccatus", "strain": "strain=DSM 45419", "accession": "GCA_900103785.1", "taxid": 1137991, "species_taxid": 1137991, "relation_to_type": "type", "validated": true, "ani": 75.2001, "matched_fragments": 163, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces angustmyceticus", "strain": "strain=NBRC 3934", "accession": "GCA_009176265.1", "taxid": 285578, "species_taxid": 285578, "relation_to_type": "type", "validated": true, "ani": 75.1942, "matched_fragments": 181, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas hominis", "strain": "strain=DSM 9581", "accession": "GCA_014201095.1", "taxid": 156981, "species_taxid": 156981, "relation_to_type": "suspected-type", "validated": true, "ani": 75.1458, "matched_fragments": 172, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomycetospora endophytica", "strain": "strain=TBRC 5722", "accession": "GCA_021026375.1", "taxid": 2291215, "species_taxid": 2291215, "relation_to_type": "type", "validated": true, "ani": 74.9998, "matched_fragments": 260, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura hibisca", "strain": "strain=NBRC 15177", "accession": "GCA_001552635.1", "taxid": 68565, "species_taxid": 68565, "relation_to_type": "type", "validated": true, "ani": 74.98, "matched_fragments": 211, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000348785.1", "gtdb_species": "s__Ilumatobacter_A coccineus", "ani": 100.0, "matched_fragments": 1608, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A", "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_000350145.1", "gtdb_species": "s__Ilumatobacter_A nonamiensis", "ani": 79.6919, "matched_fragments": 638, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A", "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_013002175.1", "gtdb_species": "s__Ilumatobacter_A sp013002175", "ani": 78.747, "matched_fragments": 488, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A", "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_018666235.1", "gtdb_species": "s__Ilumatobacter_A sp018666235", "ani": 78.187, "matched_fragments": 399, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.78", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_905182555.1", "gtdb_species": "s__Ilumatobacter_A sp905182555", "ani": 77.9153, "matched_fragments": 309, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A", "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_004364865.1", "gtdb_species": "s__Ilumatobacter fluminis", "ani": 77.8168, "matched_fragments": 545, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter", "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_013213745.1", "gtdb_species": "s__JABSQH01 sp013213745", "ani": 77.8138, "matched_fragments": 370, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01", "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_002698945.1", "gtdb_species": "s__Ilumatobacter sp002698945", "ani": 77.5843, "matched_fragments": 395, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter", "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_009704985.1", "gtdb_species": "s__VFMC01 sp009704985", "ani": 77.2776, "matched_fragments": 421, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01", "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_009650215.1", "gtdb_species": "s__Actinomarinicola tropica", "ani": 76.5114, "matched_fragments": 277, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola", "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_017577565.1", "gtdb_species": "s__ZC4RG19 sp017577565", "ani": 76.0522, "matched_fragments": 249, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19", "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_005888295.1", "gtdb_species": "s__AC-9 sp005888295", "ani": 75.667, "matched_fragments": 105, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__QHCF01;g__AC-9", "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_016862375.1", "gtdb_species": "s__Actinoplanes rishiriensis", "ani": 75.0429, "matched_fragments": 217, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes", "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_019236545.1", "gtdb_species": "s__Palsa-739 sp019236545", "ani": 74.8098, "matched_fragments": 80, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.19", "min_intra_species_ani": "98.19", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Ilumatobacter", "coccineus", "YM16-304" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }