{ "type": "genome", "identifier": "GCF_018334155.1", "organism": "Devosia litorisediminis", "title": "Devosia litorisediminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Sungkyunkwan University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018334155.1", "bioproject": "PRJNA224116", "biosample": "SAMN18825276", "wgs_master": "JAGXTP000000000.1", "refseq_category": "reference genome", "taxid": "2829817", "species_taxid": "2829817", "organism_name": "Devosia litorisediminis", "infraspecific_name": "strain=BSSL-BM10", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/10", "asm_name": "ASM1833415v1", "asm_submitter": "Sungkyunkwan University", "gbrs_paired_asm": "GCA_018334155.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/334/155/GCF_018334155.1_ASM1833415v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3743297", "genome_size_ungapped": "3743297", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018334155.1-RS_2024_05_13", "annotation_date": "2024-05-13", "total_gene_count": "3638", "protein_coding_gene_count": "3563", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-10", "dateModified": "2021-05-10", "datePublished": "2021-05-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Devosia litorisediminis" ], "sample_taxid": [ "2829817" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Boryeong" ], "sample_host_location_id": [], "data_size": "1.046 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)": "3743297", "Number of Sequences": "5", "Longest Sequences (bp)": "2671820", "N50 (bp)": "2671820", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.9", "Number of CDSs": "3609", "Average Protein Length": "312.5", "Coding Ratio (%)": "90.4", "Number of rRNAs": "2", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Devosia beringensis", "strain": "strain=S02", "accession": "GCA_014926585.1", "taxid": 2657486, "species_taxid": 2657486, "relation_to_type": "type", "validated": true, "ani": 83.0931, "matched_fragments": 834, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia ginsengisoli", "strain": "strain=Gsoil 520", "accession": "GCA_007859655.1", "taxid": 400770, "species_taxid": 400770, "relation_to_type": "type", "validated": true, "ani": 80.8048, "matched_fragments": 735, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia epidermidihirudinis", "strain": "strain=E84", "accession": "GCA_000971295.1", "taxid": 1293439, "species_taxid": 1293439, "relation_to_type": "type", "validated": true, "ani": 80.5032, "matched_fragments": 620, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia oryziradicis", "strain": "strain=G19", "accession": "GCA_016698645.1", "taxid": 2801335, "species_taxid": 2801335, "relation_to_type": "type", "validated": true, "ani": 80.3856, "matched_fragments": 671, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia psychrophila", "strain": "strain=CGMCC 1.10210", "accession": "GCA_900112505.1", "taxid": 728005, "species_taxid": 728005, "relation_to_type": "type", "validated": true, "ani": 80.1091, "matched_fragments": 671, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia psychrophila", "strain": "strain=Cr7-05", "accession": "GCA_000971275.1", "taxid": 728005, "species_taxid": 728005, "relation_to_type": "type", "validated": true, "ani": 80.1068, "matched_fragments": 658, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia naphthalenivorans", "strain": "strain=CM5-1", "accession": "GCA_003056355.1", "taxid": 2082392, "species_taxid": 2082392, "relation_to_type": "type", "validated": true, "ani": 79.9424, "matched_fragments": 610, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia salina", "strain": "strain=SCS-3", "accession": "GCA_019504385.1", "taxid": 2860336, "species_taxid": 2860336, "relation_to_type": "type", "validated": true, "ani": 79.7558, "matched_fragments": 608, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia elaeis", "strain": "strain=S37", "accession": "GCA_001650025.1", "taxid": 1770058, "species_taxid": 1770058, "relation_to_type": "type", "validated": true, "ani": 79.3245, "matched_fragments": 550, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia sediminis", "strain": "strain=MSA67", "accession": "GCA_016411825.1", "taxid": 2798801, "species_taxid": 2798801, "relation_to_type": "type", "validated": true, "ani": 79.2139, "matched_fragments": 566, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia subaequoris", "strain": "strain=HST3-14", "accession": "GCA_024158985.1", "taxid": 395930, "species_taxid": 395930, "relation_to_type": "type", "validated": true, "ani": 79.2028, "matched_fragments": 540, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia rhizoryzae", "strain": "strain=LEGU1", "accession": "GCA_016698665.1", "taxid": 2774137, "species_taxid": 2774137, "relation_to_type": "type", "validated": true, "ani": 78.73, "matched_fragments": 480, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium denitrificans", "strain": "strain=LA-28", "accession": "GCA_003403035.1", "taxid": 2294114, "species_taxid": 2294114, "relation_to_type": "type", "validated": true, "ani": 76.3459, "matched_fragments": 79, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudogemmobacter hezensis", "strain": "strain=D13-10-4-6", "accession": "GCA_013155295.1", "taxid": 2737662, "species_taxid": 2737662, "relation_to_type": "type", "validated": true, "ani": 75.9721, "matched_fragments": 60, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus isoporae", "strain": "strain=DSM 22220", "accession": "GCA_900101865.1", "taxid": 591205, "species_taxid": 591205, "relation_to_type": "type", "validated": true, "ani": 75.8696, "matched_fragments": 74, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax jejudonensis", "strain": "strain=CECT 8625", "accession": "GCA_900172265.1", "taxid": 1529041, "species_taxid": 1529041, "relation_to_type": "type", "validated": true, "ani": 75.7492, "matched_fragments": 71, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018334155.1", "gtdb_species": "s__Devosia sp018334155", "ani": 100.0, "matched_fragments": 1245, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_014926585.1", "gtdb_species": "s__Devosia sp014926585", "ani": 83.0984, "matched_fragments": 833, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_005222805.1", "gtdb_species": "s__Devosia sp005222805", "ani": 81.9501, "matched_fragments": 794, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_018828145.1", "gtdb_species": "s__Devosia sp018828145", "ani": 81.3223, "matched_fragments": 768, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_014860165.1", "gtdb_species": "s__Devosia sp014860165", "ani": 80.9041, "matched_fragments": 722, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_018820005.1", "gtdb_species": "s__Devosia sp018820005", "ani": 80.8508, "matched_fragments": 464, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_900110945.1", "gtdb_species": "s__Devosia sp900110945", "ani": 80.6524, "matched_fragments": 712, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_000971295.1", "gtdb_species": "s__Devosia epidermidihirudinis", "ani": 80.5095, "matched_fragments": 621, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_900470445.1", "gtdb_species": "s__Devosia sp900470445", "ani": 80.3914, "matched_fragments": 689, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.41", "min_intra_species_ani": "95.41", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016698645.1", "gtdb_species": "s__Devosia sp016698645", "ani": 80.3823, "matched_fragments": 671, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_003056355.1", "gtdb_species": "s__Devosia naphthalenivorans", "ani": 79.9216, "matched_fragments": 612, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_016411825.1", "gtdb_species": "s__Devosia sp016411825", "ani": 79.1979, "matched_fragments": 568, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_001427875.1", "gtdb_species": "s__Devosia sp001427875", "ani": 78.8804, "matched_fragments": 549, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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": -0.26, "cell_length": 0.157, "doubling_h": null, "growth_tmp": 26.73, "optimum_tmp": 27.125, "optimum_ph": 7.393, "genome_size": 4123393.25, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.909, "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": 0.909, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.09, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Devosia", "litorisediminis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }