{ "type": "genome", "identifier": "GCF_003058465.1", "organism": "Orrella marina", "title": "Orrella marina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Zhejiang Sci-Tech University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003058465.1", "bioproject": "PRJNA224116", "biosample": "SAMN08912484", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2163011", "species_taxid": "2163011", "organism_name": "Orrella marina", "infraspecific_name": "strain=HZ20", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/04/22", "asm_name": "ASM305846v1", "asm_submitter": "Zhejiang Sci-Tech University", "gbrs_paired_asm": "GCA_003058465.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/058/465/GCF_003058465.1_ASM305846v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4227194", "genome_size_ungapped": "4227194", "gc_percent": "55.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003058465.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3805", "protein_coding_gene_count": "3571", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-04-22", "dateModified": "2018-04-22", "datePublished": "2018-04-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Orrella marina" ], "sample_taxid": [ "2163011" ], "sample_host_organism": [ "Saccharina japonica" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: East China Sea" ], "sample_host_location_id": [], "data_size": "1.201 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)": "4227194", "Number of Sequences": "1", "Longest Sequences (bp)": "4227194", "N50 (bp)": "4227194", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "55.5", "Number of CDSs": "3833", "Average Protein Length": "313.4", "Coding Ratio (%)": "85.3", "Number of rRNAs": "9", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Orrella marina", "strain": "strain=HZ20", "accession": "GCA_003058465.1", "taxid": 2163011, "species_taxid": 2163011, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1408, "total_fragments": 1409, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bordetella flabilis", "strain": "strain=AU10664", "accession": "GCA_001676725.1", "taxid": 463014, "species_taxid": 463014, "relation_to_type": "type", "validated": true, "ani": 77.6517, "matched_fragments": 80, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella pertussis", "strain": "strain=FDAARGOS_1543", "accession": "GCA_020736265.1", "taxid": 520, "species_taxid": 520, "relation_to_type": "type", "validated": true, "ani": 77.4095, "matched_fragments": 99, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella pertussis", "strain": "strain=18323", "accession": "GCA_000306945.1", "taxid": 520, "species_taxid": 520, "relation_to_type": "type", "validated": true, "ani": 77.3996, "matched_fragments": 100, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella parapertussis", "strain": "strain=FDAARGOS_177", "accession": "GCA_001525545.2", "taxid": 519, "species_taxid": 519, "relation_to_type": "suspected-type", "validated": true, "ani": 77.213, "matched_fragments": 108, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Castellaniella defragrans", "strain": "strain=CCUG 39790", "accession": "GCA_008801975.1", "taxid": 75697, "species_taxid": 75697, "relation_to_type": "type", "validated": true, "ani": 77.141, "matched_fragments": 72, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella parapertussis", "strain": "strain=NCTC5952", "accession": "GCA_900445785.1", "taxid": 519, "species_taxid": 519, "relation_to_type": "suspected-type", "validated": true, "ani": 77.1071, "matched_fragments": 105, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kerstersia gyiorum", "strain": "strain=CCUG 47000", "accession": "GCA_008801725.1", "taxid": 206506, "species_taxid": 206506, "relation_to_type": "type", "validated": true, "ani": 77.0784, "matched_fragments": 67, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella parapertussis", "strain": "strain=FDAARGOS_1541", "accession": "GCA_020735925.1", "taxid": 519, "species_taxid": 519, "relation_to_type": "suspected-type", "validated": true, "ani": 77.0724, "matched_fragments": 109, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella avium", "strain": "strain=HAMBI_2160", "accession": "GCA_003350095.1", "taxid": 521, "species_taxid": 521, "relation_to_type": "type", "validated": true, "ani": 76.8762, "matched_fragments": 74, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Castellaniella defragrans", "strain": "strain=DSM 12141", "accession": "GCA_014203015.1", "taxid": 75697, "species_taxid": 75697, "relation_to_type": "type", "validated": true, "ani": 76.8218, "matched_fragments": 71, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kerstersia gyiorum", "strain": "strain=DSM 16618", "accession": "GCA_004216755.1", "taxid": 206506, "species_taxid": 206506, "relation_to_type": "type", "validated": true, "ani": 76.7945, "matched_fragments": 66, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella avium", "strain": "strain=ATCC 35086", "accession": "GCA_003581385.1", "taxid": 521, "species_taxid": 521, "relation_to_type": "type", "validated": true, "ani": 76.7538, "matched_fragments": 76, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sheuella amnicola", "strain": "strain=NBD-18", "accession": "GCA_010499255.1", "taxid": 2707330, "species_taxid": 2707330, "relation_to_type": "type", "validated": true, "ani": 76.7261, "matched_fragments": 62, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracandidimonas soli", "strain": "strain=DSM 100048", "accession": "GCA_004342005.1", "taxid": 1917182, "species_taxid": 1917182, "relation_to_type": "type", "validated": true, "ani": 76.6717, "matched_fragments": 81, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter animicus", "strain": "strain=LMG 26690", "accession": "GCA_902859585.1", "taxid": 1389935, "species_taxid": 1389935, "relation_to_type": "type", "validated": true, "ani": 76.5764, "matched_fragments": 93, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella bronchiseptica", "strain": "strain=NBRC 13691", "accession": "GCA_001598655.1", "taxid": 518, "species_taxid": 518, "relation_to_type": "suspected-type", "validated": true, "ani": 76.5422, "matched_fragments": 99, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corticimicrobacter populi", "strain": "strain=3d-2-2", "accession": "GCA_003123725.1", "taxid": 2175229, "species_taxid": 2175229, "relation_to_type": "type", "validated": true, "ani": 76.3919, "matched_fragments": 78, "total_fragments": 1409, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003058465.1", "gtdb_species": "s__Algicoccus marinus", "ani": 100.0, "matched_fragments": 1408, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Algicoccus", "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_001457475.1", "gtdb_species": "s__Achromobacter xylosoxidans", "ani": 78.6742, "matched_fragments": 115, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.72", "min_intra_species_ani": "96.70", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 75, "status": "-" }, { "accession": "GCF_001270295.1", "gtdb_species": "s__Achromobacter sp001270295", "ani": 77.5578, "matched_fragments": 79, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "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_000306945.1", "gtdb_species": "s__Bordetella pertussis", "ani": 77.4522, "matched_fragments": 101, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "95.13", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.83", "num_clustered_genomes": 983, "status": "-" }, { "accession": "GCF_002261345.1", "gtdb_species": "s__Bordetella_A sp002261345", "ani": 77.4273, "matched_fragments": 100, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.26", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003600685.1", "gtdb_species": "s__Achromobacter spanius_B", "ani": 77.3611, "matched_fragments": 93, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.56", "min_intra_species_ani": "98.20", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_900445835.1", "gtdb_species": "s__Bordetella avium", "ani": 77.311, "matched_fragments": 81, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.81", "min_intra_species_ani": "99.47", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 26, "status": "-" }, { "accession": "GCF_002902905.1", "gtdb_species": "s__Achromobacter sp002902905", "ani": 77.1338, "matched_fragments": 93, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.15", "min_intra_species_ani": "96.15", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002119665.1", "gtdb_species": "s__Bordetella_B sp002119665", "ani": 77.0522, "matched_fragments": 87, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_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_014170305.1", "gtdb_species": "s__Achromobacter sp014170305", "ani": 76.9522, "matched_fragments": 96, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "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_014203015.1", "gtdb_species": "s__Castellaniella defragrans", "ani": 76.8218, "matched_fragments": 71, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "98.49", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_004216755.1", "gtdb_species": "s__Kerstersia gyiorum", "ani": 76.7945, "matched_fragments": 66, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kerstersia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.96", "min_intra_species_ani": "97.89", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_010499255.1", "gtdb_species": "s__NBD-18 sp003507735", "ani": 76.7261, "matched_fragments": 62, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.47", "min_intra_species_ani": "99.47", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002966795.1", "gtdb_species": "s__Achromobacter spanius_D", "ani": 76.7126, "matched_fragments": 109, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.32", "min_intra_species_ani": "95.32", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004342005.1", "gtdb_species": "s__Paracandidimonas soli", "ani": 76.6717, "matched_fragments": 81, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paracandidimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_902859585.1", "gtdb_species": "s__Achromobacter animicus", "ani": 76.5764, "matched_fragments": 93, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.58", "min_intra_species_ani": "96.10", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_019218885.1", "gtdb_species": "s__Bordetella_A sp019218885", "ani": 76.4458, "matched_fragments": 87, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_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_003123725.1", "gtdb_species": "s__Corticimicrobacter populi", "ani": 76.3919, "matched_fragments": 78, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Corticimicrobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.49", "min_intra_species_ani": "96.49", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_902859645.1", "gtdb_species": "s__Achromobacter insuavis", "ani": 76.3275, "matched_fragments": 105, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.6014, "mean_intra_species_ani": "99.48", "min_intra_species_ani": "98.86", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_900078315.1", "gtdb_species": "s__Bordetella_B ansorpii", "ani": 76.2792, "matched_fragments": 90, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_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_000236785.1", "gtdb_species": "s__Achromobacter arsenitoxydans", "ani": 76.1714, "matched_fragments": 101, "total_fragments": 1409, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": 4848100.0, "gc_content": 67.4, "coding_genes": 4333.0, "rRNA16S_genes": null, "tRNA_genes": 49.0, "gram_stain": null, "sporulation": null, "motility": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Orrella", "marina" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }