{ "type": "genome", "identifier": "GCA_011682415.1", "organism": "Pseudomonadota bacterium", "title": "Pseudomonadota bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Ocean University of China", "publication": [ {} ], "properties": { "assembly_accession": "GCA_011682415.1", "bioproject": "PRJNA514953", "biosample": "SAMN13826946", "wgs_master": "JAACEQ000000000.1", "refseq_category": "na", "taxid": "1977087", "species_taxid": "1977087", "organism_name": "Pseudomonadota bacterium", "infraspecific_name": "", "isolate": "OTbin.78", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/23", "asm_name": "ASM1168241v1", "submitter": "Ocean University of China", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/011/682/415/GCA_011682415.1_ASM1168241v1", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-23", "dateModified": "2020-03-23", "datePublished": "2020-03-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonadota bacterium" ], "sample_taxid": [ "1977087" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.534 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 78.03, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1883571", "Number of Sequences": "274", "Longest Sequences (bp)": "22007", "N50 (bp)": "8053", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.8", "Number of CDSs": "1418", "Average Protein Length": "319.0", "Coding Ratio (%)": "72.0", "Number of rRNAs": "0", "Number of tRNAs": "28", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfogranum mediterraneum", "strain": "strain=DSM 13871", "accession": "GCA_000429965.1", "taxid": 160661, "species_taxid": 160661, "relation_to_type": "type", "validated": true, "ani": 76.8416, "matched_fragments": 79, "total_fragments": 491, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobulbus elongatus", "strain": "strain=DSM 2908", "accession": "GCA_000621145.1", "taxid": 53332, "species_taxid": 53332, "relation_to_type": "type", "validated": true, "ani": 76.5235, "matched_fragments": 83, "total_fragments": 491, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobulbus propionicus", "strain": "strain=DSM 2032", "accession": "GCA_000186885.1", "taxid": 894, "species_taxid": 894, "relation_to_type": "type", "validated": true, "ani": 76.2486, "matched_fragments": 76, "total_fragments": 491, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfoprunum benzoelyticum", "strain": "strain=DSM 28570", "accession": "GCA_016918515.1", "taxid": 1506996, "species_taxid": 1506996, "relation_to_type": "type", "validated": true, "ani": 75.8967, "matched_fragments": 50, "total_fragments": 491, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfoprunum benzoelyticum", "strain": "strain=DSM 28570", "accession": "GCA_014201505.1", "taxid": 1506996, "species_taxid": 1506996, "relation_to_type": "type", "validated": true, "ani": 75.8967, "matched_fragments": 50, "total_fragments": 491, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 78.03, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_002897615.1", "gtdb_species": "s__BMS3Abin13 sp002897615", "ani": 95.883, "matched_fragments": 452, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__BMS3Abin13", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.72", "min_intra_species_ani": "95.88", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCA_013151365.1", "gtdb_species": "s__BMS3Abin13 sp013151365", "ani": 92.3378, "matched_fragments": 397, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__BMS3Abin13", "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_015484845.1", "gtdb_species": "s__DRKI01 sp015484845", "ani": 77.847, "matched_fragments": 140, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01", "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_011051875.1", "gtdb_species": "s__DRKI01 sp011051875", "ani": 77.4021, "matched_fragments": 113, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.14", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_011372855.1", "gtdb_species": "s__UBA10518 sp011372855", "ani": 77.1882, "matched_fragments": 98, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518", "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_003604995.1", "gtdb_species": "s__UBA10518 sp003604995", "ani": 77.1244, "matched_fragments": 99, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518", "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_903842475.1", "gtdb_species": "s__Desulfobulbus sp903842475", "ani": 76.9551, "matched_fragments": 55, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus", "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_000429965.1", "gtdb_species": "s__Desulfobulbus_A mediterraneus", "ani": 76.8416, "matched_fragments": 79, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_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_015486315.1", "gtdb_species": "s__Desulfobulbus_C sp015486315", "ani": 76.4953, "matched_fragments": 57, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_C", "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_000186885.1", "gtdb_species": "s__Desulfobulbus propionicus", "ani": 76.2486, "matched_fragments": 76, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus", "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_017998195.1", "gtdb_species": "s__Desulfobulbus sp017998195", "ani": 76.1992, "matched_fragments": 65, "total_fragments": 491, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus", "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": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Desulfobacterota", "c__Desulfobulbia", "o__Desulfobulbales", "f__Desulfobulbaceae", "g__BMS3Abin13", "s__BMS3Abin13 sp002897615" ], "_genome_taxon": [ "Pseudomonadota", "bacterium", "d__Bacteria", "p__Desulfobacterota", "c__Desulfobulbia", "o__Desulfobulbales", "f__Desulfobulbaceae", "g__BMS3Abin13", "s__BMS3Abin13 sp002897615", "Bacteria", "Desulfobacterota", "Desulfobulbia", "Desulfobulbales", "Desulfobulbaceae", "BMS3Abin13", "BMS3Abin13", "sp002897615" ], "_meo": [ { "id": "MEO_0000686", "label": "hydrothermal sediment" }, { "id": "MEO_0000031", "label": "hydrothermal vent" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }