{ "type": "genome", "identifier": "GCF_003387155.1", "organism": "Roseateles depolymerans", "title": "Roseateles depolymerans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003387155.1", "bioproject": "PRJNA224116", "biosample": "SAMN09064162", "wgs_master": "QUMT00000000.1", "refseq_category": "na", "taxid": "76731", "species_taxid": "76731", "organism_name": "Roseateles depolymerans", "infraspecific_name": "strain=DSM 11813", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/14", "asm_name": "ASM338715v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003387155.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/387/155/GCF_003387155.1_ASM338715v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5656781", "genome_size_ungapped": "5656401", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "13", "contig_count": "13", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003387155.1-RS_2024_09_19", "annotation_date": "2024-09-19", "total_gene_count": "4931", "protein_coding_gene_count": "4835", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-14", "dateModified": "2018-08-14", "datePublished": "2018-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Roseateles depolymerans" ], "sample_taxid": [ "76731" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Hanamuro river" ], "sample_host_location_id": [], "data_size": "1.551 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)": "5656781", "Number of Sequences": "13", "Longest Sequences (bp)": "1816172", "N50 (bp)": "1369052", "Gap Ratio (%)": "0.006718", "GCcontent (%)": "66.6", "Number of CDSs": "4941", "Average Protein Length": "340.0", "Coding Ratio (%)": "89.1", "Number of rRNAs": "2", "Number of tRNAs": "59", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Roseateles depolymerans", "strain": "strain=DSM 11813", "accession": "GCA_003387155.1", "taxid": 76731, "species_taxid": 76731, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1877, "total_fragments": 1878, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Roseateles terrae", "strain": "strain=CECT 7247", "accession": "GCA_014192155.1", "taxid": 431060, "species_taxid": 431060, "relation_to_type": "type", "validated": true, "ani": 87.0692, "matched_fragments": 1542, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mitsuaria chitinivorans", "strain": "strain=HWN-4", "accession": "GCA_002761755.1", "taxid": 2917965, "species_taxid": 2917965, "relation_to_type": "type", "validated": true, "ani": 82.5784, "matched_fragments": 1112, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelomonas puraquae", "strain": "strain=CCUG 52769", "accession": "GCA_002205845.1", "taxid": 431059, "species_taxid": 431059, "relation_to_type": "type", "validated": true, "ani": 80.1548, "matched_fragments": 778, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelomonas saccharophila", "strain": "strain=DSM 654", "accession": "GCA_004342485.1", "taxid": 304, "species_taxid": 304, "relation_to_type": "type", "validated": true, "ani": 80.0854, "matched_fragments": 747, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ideonella dechloratans", "strain": "strain=CCUG 30977", "accession": "GCA_021049305.1", "taxid": 36863, "species_taxid": 36863, "relation_to_type": "type", "validated": true, "ani": 79.8622, "matched_fragments": 604, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paucibacter toxinivorans", "strain": "strain=DSM 16998", "accession": "GCA_004362525.1", "taxid": 270368, "species_taxid": 270368, "relation_to_type": "type", "validated": true, "ani": 79.6511, "matched_fragments": 684, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ideonella azotifigens", "strain": "strain=DSM 21438", "accession": "GCA_006519715.1", "taxid": 513160, "species_taxid": 513160, "relation_to_type": "type", "validated": true, "ani": 79.6197, "matched_fragments": 537, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ideonella benzenivorans", "strain": "strain=B7", "accession": "GCA_020387415.1", "taxid": 2831643, "species_taxid": 2831643, "relation_to_type": "type", "validated": true, "ani": 79.526, "matched_fragments": 602, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Schlegelella thermodepolymerans", "strain": "strain=DSM 15344", "accession": "GCA_015476235.1", "taxid": 215580, "species_taxid": 215580, "relation_to_type": "type", "validated": true, "ani": 79.3698, "matched_fragments": 541, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Schlegelella thermodepolymerans", "strain": "strain=DSM 15344", "accession": "GCA_002933415.1", "taxid": 215580, "species_taxid": 215580, "relation_to_type": "type", "validated": true, "ani": 79.3697, "matched_fragments": 532, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphaerotilus natans", "strain": "strain=ATCC 13338", "accession": "GCA_900156335.1", "taxid": 34103, "species_taxid": 34103, "relation_to_type": "type", "validated": true, "ani": 79.2682, "matched_fragments": 568, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphaerotilus hippei", "strain": "strain=DSM 566", "accession": "GCA_003201595.1", "taxid": 744406, "species_taxid": 744406, "relation_to_type": "type", "validated": true, "ani": 79.2578, "matched_fragments": 538, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azohydromonas caseinilytica", "strain": "strain=G-1-1-14", "accession": "GCA_012927045.1", "taxid": 2728836, "species_taxid": 2728836, "relation_to_type": "type", "validated": true, "ani": 78.8812, "matched_fragments": 639, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Schlegelella brevitalea", "strain": "strain=DSM 7029", "accession": "GCA_001017435.1", "taxid": 413882, "species_taxid": 413882, "relation_to_type": "type", "validated": true, "ani": 78.7459, "matched_fragments": 525, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter humi", "strain": "strain=18x22-1", "accession": "GCA_004681975.1", "taxid": 2530451, "species_taxid": 2530451, "relation_to_type": "type", "validated": true, "ani": 78.6684, "matched_fragments": 491, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003387155.1", "gtdb_species": "s__Roseateles depolymerans", "ani": 100.0, "matched_fragments": 1877, "total_fragments": 1878, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Roseateles", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_014192155.1", "gtdb_species": "s__Roseateles terrae", "ani": 87.0818, "matched_fragments": 1540, "total_fragments": 1878, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Roseateles", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900109745.1", "gtdb_species": "s__Roseateles sp900109745", "ani": 84.4004, 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"d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria", "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": -0.061, "cell_length": 0.301, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 35.0, "optimum_ph": null, "genome_size": 5681721.6, "gc_content": 66.584, "coding_genes": 4684.667, "rRNA16S_genes": 4.0, "tRNA_genes": 58.0, "gram_stain": 0.0, "sporulation": null, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Roseateles", "depolymerans" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }