{ "type": "genome", "identifier": "GCF_000423085.1", "organism": "Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570", "title": "Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000423085.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440835", "wgs_master": "AUHH00000000.1", "refseq_category": "na", "taxid": "1121933", "species_taxid": "266854", "organism_name": "Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570", "infraspecific_name": "strain=DSM 17626", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/11", "asm_name": "ASM42308v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000423085.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/423/085/GCF_000423085.1_ASM42308v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4117723", "genome_size_ungapped": "4112232", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "74", "contig_count": "81", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000423085.1-RS_2024_05_15", "annotation_date": "2024-05-15", "total_gene_count": "3859", "protein_coding_gene_count": "3753", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-11", "dateModified": "2013-07-11", "datePublished": "2013-07-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570" ], "sample_taxid": [ "1121933" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Singapore" ], "sample_host_location_id": [], "data_size": "1.121 MB", "sample_ph_range": { "min": 5085.0, "max": 5085.0 }, "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)": "4117723", "Number of Sequences": "74", "Longest Sequences (bp)": "277336", "N50 (bp)": "88652", "Gap Ratio (%)": "0.133350", "GCcontent (%)": "69.0", "Number of CDSs": "3801", "Average Protein Length": "323.9", "Coding Ratio (%)": "89.7", "Number of rRNAs": "2", "Number of tRNAs": "58", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Granulicoccus phenolivorans", "strain": "strain=DSM 17626", "accession": "GCA_000423085.1", "taxid": 266854, "species_taxid": 266854, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1335, "total_fragments": 1338, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Granulicoccus phenolivorans", "strain": "strain=NBRC 107789", "accession": "GCA_001552335.1", "taxid": 266854, "species_taxid": 266854, "relation_to_type": "type", "validated": true, "ani": 99.9909, "matched_fragments": 1302, "total_fragments": 1338, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enemella evansiae", "strain": "strain=NML 020265", "accession": "GCA_002250705.1", "taxid": 2016499, "species_taxid": 2016499, "relation_to_type": "type", "validated": true, "ani": 78.8388, "matched_fragments": 456, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enemella dayhoffiae", "strain": "strain=NML 130396", "accession": "GCA_002250625.1", "taxid": 2016507, "species_taxid": 2016507, "relation_to_type": "type", "validated": true, "ani": 78.7374, "matched_fragments": 459, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Propioniciclava coleopterorum", "strain": "strain=HDW11", "accession": "GCA_011393335.1", "taxid": 2714937, "species_taxid": 2714937, "relation_to_type": "type", "validated": true, "ani": 78.4743, "matched_fragments": 299, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desertihabitans aurantiacus", "strain": "strain=CPCC 204711", "accession": "GCA_003344635.1", "taxid": 2282477, "species_taxid": 2282477, "relation_to_type": "type", "validated": true, "ani": 78.0781, "matched_fragments": 310, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Raineyella antarctica", "strain": "strain=LZ-22", "accession": "GCA_900092135.1", "taxid": 1577474, "species_taxid": 1577474, "relation_to_type": "type", "validated": true, "ani": 78.0729, "matched_fragments": 336, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desertihabitans brevis", "strain": "strain=16Sb5-5", "accession": "GCA_003327535.1", "taxid": 2268447, "species_taxid": 2268447, "relation_to_type": "type", "validated": true, "ani": 77.8638, "matched_fragments": 363, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Auraticoccus monumenti", "strain": "strain=MON 2.2", "accession": "GCA_900101785.1", "taxid": 675864, "species_taxid": 675864, "relation_to_type": "type", "validated": true, "ani": 77.8507, "matched_fragments": 336, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Auraticoccus cholistanensis", "strain": "strain=F435", "accession": "GCA_009742705.1", "taxid": 2656650, "species_taxid": 2656650, "relation_to_type": "type", "validated": true, "ani": 77.7263, "matched_fragments": 330, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microlunatus kandeliicorticis", "strain": "strain=DSM 100723", "accession": "GCA_014137855.1", "taxid": 1759536, "species_taxid": 1759536, "relation_to_type": "type", "validated": true, "ani": 77.7255, "matched_fragments": 325, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Propioniciclava soli", "strain": "strain=YIM S02567", "accession": "GCA_014858005.1", "taxid": 2775081, "species_taxid": 2775081, "relation_to_type": "type", "validated": true, "ani": 77.6962, "matched_fragments": 234, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microlunatus parietis", "strain": "strain=DSM 22083", "accession": "GCA_013407955.1", "taxid": 682979, "species_taxid": 682979, "relation_to_type": "type", "validated": true, "ani": 77.1663, "matched_fragments": 371, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tessaracoccus defluvii", "strain": "strain=JCM 17540", "accession": "GCA_014489575.1", "taxid": 1285901, "species_taxid": 1285901, "relation_to_type": "type", "validated": true, "ani": 77.0509, "matched_fragments": 229, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kribbella turkmenica", "strain": "strain=16K104", "accession": "GCA_004348725.1", "taxid": 2530375, "species_taxid": 2530375, "relation_to_type": "type", "validated": true, "ani": 76.8785, "matched_fragments": 278, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides donggukensis", "strain": "strain=MJB4", "accession": "GCA_014842875.1", "taxid": 2774019, "species_taxid": 2774019, "relation_to_type": "type", "validated": true, "ani": 76.8203, "matched_fragments": 240, "total_fragments": 1338, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000423085.1", "gtdb_species": "s__Granulicoccus phenolivorans", "ani": 100.0, "matched_fragments": 1335, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Granulicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_002250625.1", "gtdb_species": "s__Enemella sp002250625", "ani": 78.7294, "matched_fragments": 460, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "98.13", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004362375.1", "gtdb_species": "s__Enemella evansiae", "ani": 78.625, "matched_fragments": 472, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.12", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_900092135.1", "gtdb_species": "s__Raineyella antarctica", "ani": 78.1036, "matched_fragments": 333, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Raineyella", "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_003344635.1", "gtdb_species": "s__Desertihabitans aurantiacus", "ani": 78.0748, "matched_fragments": 311, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.17", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900101785.1", "gtdb_species": "s__Auraticoccus monumenti", "ani": 77.8317, "matched_fragments": 338, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus", "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_009742705.1", "gtdb_species": "s__Auraticoccus cholistanensis", "ani": 77.7255, "matched_fragments": 330, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus", "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_014137855.1", "gtdb_species": "s__Friedmanniella_A endophytica", "ani": 77.721, "matched_fragments": 323, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_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_013408315.1", "gtdb_species": "s__Microlunatus_A terrae", "ani": 77.6316, "matched_fragments": 342, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_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_007362775.1", "gtdb_species": "s__Microlunatus_A sp007362775", "ani": 77.5835, "matched_fragments": 297, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_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_013693855.1", "gtdb_species": "s__Micropruina sp013693855", "ani": 77.5275, "matched_fragments": 268, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina", "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_012839035.1", "gtdb_species": "s__Enemella sp012839035", "ani": 77.4952, "matched_fragments": 241, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella", "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_900105785.1", "gtdb_species": "s__Friedmanniella sagamiharensis", "ani": 77.4119, "matched_fragments": 286, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella", "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_018715445.1", "gtdb_species": "s__Avipropionibacterium avicola", "ani": 77.2613, "matched_fragments": 213, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Avipropionibacterium", "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_017876495.1", "gtdb_species": "s__Friedmanniella capsulata", "ani": 77.2141, "matched_fragments": 364, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella", "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_900105385.1", "gtdb_species": "s__Microlunatus_A soli", "ani": 77.2083, "matched_fragments": 325, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_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_013407955.1", "gtdb_species": "s__Microlunatus_B parietis", "ani": 77.1572, "matched_fragments": 374, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B", "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_018531445.1", "gtdb_species": "s__Pseudonocardia sp018531445", "ani": 75.9642, "matched_fragments": 317, "total_fragments": 1338, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": -0.523, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 30.0, "optimum_ph": 7.0, "genome_size": 3766493.75, "gc_content": 69.295, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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": [ "Granulicoccus", "phenolivorans", "DSM", "17626", "=", "NBRC", "107789", "=", "JCM", "15570" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }