{ "type": "genome", "identifier": "GCF_003148475.1", "organism": "Pseudaminobacter salicylatoxidans", "title": "Pseudaminobacter salicylatoxidans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003148475.1", "bioproject": "PRJNA224116", "biosample": "SAMN08770120", "wgs_master": "QGGG00000000.1", "refseq_category": "reference genome", "taxid": "93369", "species_taxid": "93369", "organism_name": "Pseudaminobacter salicylatoxidans", "infraspecific_name": "strain=DSM 6986", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/22", "asm_name": "ASM314847v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003148475.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/148/475/GCF_003148475.1_ASM314847v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4836797", "genome_size_ungapped": "4836411", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "43", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003148475.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "4760", "protein_coding_gene_count": "4628", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-22", "dateModified": "2018-05-22", "datePublished": "2018-05-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudaminobacter salicylatoxidans" ], "sample_taxid": [ "93369" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.345 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)": "4836797", "Number of Sequences": "43", "Longest Sequences (bp)": "582227", "N50 (bp)": "232367", "Gap Ratio (%)": "0.007980", "GCcontent (%)": "62.7", "Number of CDSs": "4700", "Average Protein Length": "304.3", "Coding Ratio (%)": "88.7", "Number of rRNAs": "3", "Number of tRNAs": "56", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mesorhizobium zhangyense", "strain": "strain=CGMCC 1.15528", "accession": "GCA_011045115.1", "taxid": 1776730, "species_taxid": 1776730, "relation_to_type": "type", "validated": true, "ani": 81.6517, "matched_fragments": 873, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aminobacter aganoensis", "strain": "strain=DSM 7051", "accession": "GCA_014206975.1", "taxid": 83264, "species_taxid": 83264, "relation_to_type": "type", "validated": true, "ani": 80.9717, "matched_fragments": 763, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aminobacter niigataensis", "strain": "strain=DSM 7050", "accession": "GCA_014200015.1", "taxid": 83265, "species_taxid": 83265, "relation_to_type": "type", "validated": true, "ani": 80.7907, "matched_fragments": 745, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquamicrobium defluvii", "strain": "strain=DSM 11603", "accession": "GCA_004363725.1", "taxid": 69279, "species_taxid": 69279, "relation_to_type": "type", "validated": true, "ani": 80.4899, "matched_fragments": 626, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium hawassense", "strain": "strain=AC99b", "accession": "GCA_003289945.1", "taxid": 1209954, "species_taxid": 1209954, "relation_to_type": "type", "validated": true, "ani": 80.4646, "matched_fragments": 752, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aminobacter ciceronei", "strain": "strain=DSM 17455", "accession": "GCA_014138635.1", "taxid": 150723, "species_taxid": 150723, "relation_to_type": "type", "validated": true, "ani": 80.4641, "matched_fragments": 747, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium composti", "strain": "strain=CC-YTH430", "accession": "GCA_004801285.1", "taxid": 2675109, "species_taxid": 2675109, "relation_to_type": "type", "validated": true, "ani": 80.4341, 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium caraganae", "strain": "strain=LMG 24397", "accession": "GCA_016836705.1", "taxid": 483206, "species_taxid": 483206, "relation_to_type": "type", "validated": true, "ani": 80.2754, "matched_fragments": 772, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium intechi", "strain": "strain=BD68", "accession": "GCA_002879535.2", "taxid": 537601, "species_taxid": 537601, "relation_to_type": "type", "validated": true, "ani": 80.263, "matched_fragments": 705, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium norvegicum", "strain": "strain=10.2.2", "accession": "GCA_004919685.1", "taxid": 1085774, "species_taxid": 1085774, "relation_to_type": "type", "validated": true, "ani": 80.2548, "matched_fragments": 776, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium erdmanii", "strain": "strain=USDA 3471", "accession": "GCA_000472705.1", "taxid": 1777866, "species_taxid": 1777866, "relation_to_type": "type", "validated": true, "ani": 80.2525, "matched_fragments": 731, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium metallidurans", "strain": "strain=STM 2683", "accession": "GCA_000350085.1", "taxid": 489722, "species_taxid": 489722, "relation_to_type": "type", "validated": true, "ani": 80.2217, "matched_fragments": 731, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium sophorae", "strain": "strain=ICMP 19535", "accession": "GCA_002270415.1", "taxid": 1300294, "species_taxid": 1300294, "relation_to_type": "type", "validated": true, "ani": 80.2054, "matched_fragments": 744, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium opportunistum", "strain": "strain=WSM2075", "accession": "GCA_000176035.2", "taxid": 593909, "species_taxid": 593909, "relation_to_type": "type", "validated": true, "ani": 80.1725, "matched_fragments": 763, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium comanense", "strain": "strain=3P27G6", "accession": "GCA_005503535.1", "taxid": 2502215, "species_taxid": 2502215, "relation_to_type": "type", "validated": true, "ani": 80.1233, "matched_fragments": 777, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquamicrobium lusatiense", "strain": "strain=DSM 11099", "accession": "GCA_014201615.1", "taxid": 89772, "species_taxid": 89772, "relation_to_type": "type", "validated": true, "ani": 80.0789, "matched_fragments": 615, "total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium albiziae", "strain": "strain=DSM 21822", 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"total_fragments": 1591, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003148475.1", "gtdb_species": "s__Pseudaminobacter salicylatoxidans", "ani": 100.0, "matched_fragments": 1589, "total_fragments": 1591, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.95", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003012705.1", "gtdb_species": "s__Pseudaminobacter soli", "ani": 84.4228, "matched_fragments": 1012, "total_fragments": 1591, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter", "ani_circumscription_radius": 95.0, 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