{ "type": "genome", "identifier": "GCF_013155295.1", "organism": "Pseudogemmobacter hezensis", "title": "Pseudogemmobacter hezensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Institute of Forest Ecology Environment and Protection", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013155295.1", "bioproject": "PRJNA224116", "biosample": "SAMN14918901", "wgs_master": "JABJXT000000000.1", "refseq_category": "reference genome", "taxid": "2737662", "species_taxid": "2737662", "organism_name": "Pseudogemmobacter hezensis", "infraspecific_name": "strain=D13-10-4-6", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/05/24", "asm_name": "ASM1315529v1", "asm_submitter": "Research Institute of Forest Ecology Environment and Protection", "gbrs_paired_asm": "GCA_013155295.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/155/295/GCF_013155295.1_ASM1315529v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4605234", "genome_size_ungapped": "4605214", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "64", "contig_count": "64", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013155295.1-RS_2024_07_17", "annotation_date": "2024-07-17", "total_gene_count": "4388", "protein_coding_gene_count": "4249", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-05-24", "dateModified": "2020-05-24", "datePublished": "2020-05-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudogemmobacter hezensis" ], "sample_taxid": [ "2737662" ], "sample_host_organism": [ "poplar" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Puyang" ], "sample_host_location_id": [], "data_size": "1.274 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)": "4605234", "Number of Sequences": "64", "Longest Sequences (bp)": "456438", "N50 (bp)": "204909", "Gap Ratio (%)": "0.000434", "GCcontent (%)": "62.9", "Number of CDSs": "4344", "Average Protein Length": "309.7", "Coding Ratio (%)": "87.6", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1501, "total_fragments": 1506, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudogemmobacter bohemicus", "strain": "strain=Cd-10", "accession": "GCA_003290025.1", "taxid": 2250708, "species_taxid": 2250708, "relation_to_type": "type", "validated": true, "ani": 83.5767, "matched_fragments": 972, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter serpentinus", "strain": "strain=HB-1", "accession": "GCA_008973825.1", "taxid": 2652247, "species_taxid": 2652247, "relation_to_type": "type", "validated": true, "ani": 78.8629, "matched_fragments": 508, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter caeruleus", "strain": "strain=N8", "accession": "GCA_008271655.1", "taxid": 2595004, "species_taxid": 2595004, "relation_to_type": "type", "validated": true, "ani": 78.5598, "matched_fragments": 510, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter caeni", "strain": "strain=DSM 21823", "accession": "GCA_003054195.1", "taxid": 589035, "species_taxid": 589035, "relation_to_type": "type", "validated": true, "ani": 78.5306, "matched_fragments": 458, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquatilis", "strain": "strain=DSM 3857", "accession": "GCA_900110025.1", "taxid": 933059, "species_taxid": 933059, "relation_to_type": "type", "validated": true, "ani": 78.4904, "matched_fragments": 478, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter caeni", "strain": "strain=CGMCC 1.7745", "accession": "GCA_007830625.1", "taxid": 589035, "species_taxid": 589035, "relation_to_type": "type", "validated": true, "ani": 78.4807, "matched_fragments": 461, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter lanyuensis", "strain": "strain=KCTC 23714", "accession": "GCA_014652355.1", "taxid": 1054497, "species_taxid": 1054497, "relation_to_type": "type", "validated": true, "ani": 78.3918, "matched_fragments": 431, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter fulva", "strain": "strain=con5", "accession": "GCA_018798885.1", "taxid": 2840474, "species_taxid": 2840474, "relation_to_type": "type", "validated": true, "ani": 78.3906, "matched_fragments": 504, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola algicola", "strain": "strain=ETT8", "accession": "GCA_010915705.1", "taxid": 2709381, "species_taxid": 2709381, "relation_to_type": "type", "validated": true, "ani": 78.164, "matched_fragments": 377, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter calidifons", "strain": "strain=M37P", "accession": "GCA_011174775.1", "taxid": 2715277, "species_taxid": 2715277, "relation_to_type": "type", "validated": true, "ani": 78.1172, "matched_fragments": 409, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola alkalilacus", "strain": "strain=DJC", "accession": "GCA_003443995.1", "taxid": 2305252, "species_taxid": 2305252, "relation_to_type": "type", "validated": true, "ani": 78.1141, "matched_fragments": 449, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter flagellatus", "strain": "strain=SYSU G03088", "accession": "GCA_008271465.1", "taxid": 2593021, "species_taxid": 2593021, "relation_to_type": "type", "validated": true, "ani": 77.999, "matched_fragments": 391, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_009908265.2", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 77.9403, "matched_fragments": 389, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola sediminis", "strain": "strain=DRYC-M-16", "accession": "GCA_004745575.1", "taxid": 2486418, "species_taxid": 2486418, "relation_to_type": "type", "validated": true, "ani": 77.9051, "matched_fragments": 376, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter tardus", "strain": "strain=CYK-10", "accession": "GCA_009925085.1", "taxid": 2699202, "species_taxid": 2699202, "relation_to_type": "type", "validated": true, "ani": 77.8776, "matched_fragments": 403, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter straminiformis", "strain": "strain=CAM-8", "accession": "GCA_014243445.1", "taxid": 2045119, "species_taxid": 2045119, "relation_to_type": "type", "validated": true, "ani": 77.8464, "matched_fragments": 387, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter azotoformans", "strain": "strain=KA25", "accession": "GCA_003050905.1", "taxid": 43057, "species_taxid": 43057, "relation_to_type": "type", "validated": true, "ani": 77.6929, "matched_fragments": 355, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sediminicola", "strain": "strain=JA983", "accession": "GCA_007668225.1", "taxid": 2584941, "species_taxid": 2584941, "relation_to_type": "type", "validated": true, "ani": 77.5234, "matched_fragments": 342, "total_fragments": 1506, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013155295.1", "gtdb_species": "s__Pseudogemmobacter sp013155295", "ani": 100.0, "matched_fragments": 1501, "total_fragments": 1506, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter", "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_003290025.1", "gtdb_species": "s__Pseudogemmobacter bohemicus", "ani": 83.584, "matched_fragments": 970, "total_fragments": 1506, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter", "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_016405985.1", "gtdb_species": "s__Pseudogemmobacter sp016405985", "ani": 83.2768, "matched_fragments": 935, "total_fragments": 1506, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter", "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_900105075.1", "gtdb_species": "s__Pseudogemmobacter sp900105075", "ani": 83.2015, "matched_fragments": 920, "total_fragments": 1506, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter", "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_900609055.1", "gtdb_species": "s__Pseudogemmobacter humi", "ani": 81.0018, "matched_fragments": 750, "total_fragments": 1506, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter", "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_010915705.1", "gtdb_species": "s__ETT8 sp010915705", "ani": 78.1482, "matched_fragments": 378, "total_fragments": 1506, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8", "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 }, "_genome_taxon": [ "Pseudogemmobacter", "hezensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }