{ "type": "genome", "identifier": "GCF_003985135.1", "organism": "Rhizobium fabae", "title": "Rhizobium fabae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "North West Agriculture and Forestry University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003985135.1", "bioproject": "PRJNA224116", "biosample": "SAMN10386394", "wgs_master": "RJJU00000000.1", "refseq_category": "reference genome", "taxid": "573179", "species_taxid": "573179", "organism_name": "Rhizobium fabae", "infraspecific_name": "strain=CCBAU 33202", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/28", "asm_name": "ASM398513v1", "asm_submitter": "North West Agriculture and Forestry University", "gbrs_paired_asm": "GCA_003985135.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/985/135/GCF_003985135.1_ASM398513v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6611877", "genome_size_ungapped": "6611847", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "41", "contig_count": "44", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003985135.1-RS_2024_05_01", "annotation_date": "2024-05-01", "total_gene_count": "6513", "protein_coding_gene_count": "6283", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-28", "dateModified": "2018-12-28", "datePublished": "2018-12-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium fabae" ], "sample_taxid": [ "573179" ], "sample_host_organism": [ "Vicia faba" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Nanchang." ], "sample_host_location_id": [], "data_size": "1.846 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)": "6611877", "Number of Sequences": "41", "Longest Sequences (bp)": "590525", "N50 (bp)": "379018", "Gap Ratio (%)": "0.000454", "GCcontent (%)": "61.1", "Number of CDSs": "6415", "Average Protein Length": "299.9", "Coding Ratio (%)": "87.3", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium fabae", "strain": "strain=CCBAU 33202", "accession": "GCA_003985135.1", "taxid": 573179, "species_taxid": 573179, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2171, 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"organism_name": "Rhizobium anhuiense", "strain": "strain=CGMCC 1.12621", "accession": "GCA_014638185.1", "taxid": 1184720, "species_taxid": 1184720, "relation_to_type": "type", "validated": true, "ani": 88.9575, "matched_fragments": 1717, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium indicum", "strain": "strain=JKLM 12A2", "accession": "GCA_005862305.2", "taxid": 2583231, "species_taxid": 2583231, "relation_to_type": "type", "validated": true, "ani": 88.6171, "matched_fragments": 1670, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium ruizarguesonis", "strain": "strain=UPM1133", "accession": "GCA_012349115.1", "taxid": 2081791, "species_taxid": 2081791, "relation_to_type": "type", "validated": true, "ani": 88.5968, "matched_fragments": 1676, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium sophorae", "strain": "strain=CCBAU 03386", "accession": "GCA_013087515.1", "taxid": 1535242, "species_taxid": 1535242, "relation_to_type": "type", "validated": true, "ani": 88.4369, "matched_fragments": 1655, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium chutanense", "strain": "strain=C5", "accession": "GCA_002531935.1", "taxid": 2035448, "species_taxid": 2035448, "relation_to_type": "type", "validated": true, "ani": 88.4117, "matched_fragments": 1635, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium laguerreae", "strain": "strain=FB206", "accession": "GCA_002008165.1", "taxid": 1076926, "species_taxid": 1076926, "relation_to_type": "type", "validated": true, "ani": 88.2695, "matched_fragments": 1635, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium ecuadorense", "strain": "strain=CNPSO 671", "accession": "GCA_001187535.1", "taxid": 1671795, "species_taxid": 1671795, "relation_to_type": "type", "validated": true, "ani": 88.2288, "matched_fragments": 1535, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium redzepovicii", "strain": "strain=18T", "accession": "GCA_019793435.1", "taxid": 2867518, "species_taxid": 2867518, "relation_to_type": "type", "validated": true, "ani": 88.0355, "matched_fragments": 1632, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium croatiense", "strain": "strain=13T", "accession": "GCA_019793465.1", "taxid": 2867516, "species_taxid": 2867516, "relation_to_type": "type", "validated": true, "ani": 87.8251, "matched_fragments": 1536, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium lentis", "strain": "strain=BLR27", "accession": "GCA_019684715.1", "taxid": 1138194, "species_taxid": 1138194, "relation_to_type": "type", "validated": true, "ani": 87.5151, "matched_fragments": 1572, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium viscosum", "strain": "strain=DSM 7307", "accession": "GCA_014873945.1", "taxid": 1673, "species_taxid": 1673, "relation_to_type": "type", "validated": true, "ani": 83.4087, "matched_fragments": 1349, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium mongolense subsp. loessense", "strain": "strain=CGMCC 1.3401", "accession": "GCA_900099775.1", "taxid": 158890, "species_taxid": 57676, "relation_to_type": "type", "validated": true, "ani": 81.7149, "matched_fragments": 1123, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium dioscoreae", "strain": "strain=S-93", "accession": "GCA_009176305.1", "taxid": 2653122, "species_taxid": 2653122, "relation_to_type": "type", "validated": true, "ani": 80.6991, "matched_fragments": 973, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella pollutisoli", "strain": "strain=KCTC 52677", "accession": "GCA_024609765.1", "taxid": 2250594, "species_taxid": 2250594, "relation_to_type": "type", "validated": true, "ani": 80.2782, "matched_fragments": 720, "total_fragments": 2186, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003938655.1", "gtdb_species": "s__Rhizobium pisi", "ani": 97.6128, "matched_fragments": 1965, "total_fragments": 2186, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.78", "min_intra_species_ani": "97.55", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": 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88.9258, "matched_fragments": 1563, "total_fragments": 2186, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_004123835.1", "gtdb_species": "s__Rhizobium leguminosarum_M", "ani": 88.7106, "matched_fragments": 1612, "total_fragments": 2186, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_014193025.1", "gtdb_species": "s__Rhizobium sp014193025", "ani": 88.6818, "matched_fragments": 1559, 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