{ "type": "genome", "identifier": "GCF_001651855.1", "organism": "Sinorhizobium americanum", "title": "Sinorhizobium americanum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ensifer americanum CFNEI 156T", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001651855.1", "bioproject": "PRJNA224116", "biosample": "SAMN04274562", "wgs_master": "LNQC00000000.1", "refseq_category": "na", "taxid": "194963", "species_taxid": "194963", "organism_name": "Sinorhizobium americanum", "infraspecific_name": "strain=CFNEI 156", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/05/25", "asm_name": "ASM165185v1", "asm_submitter": "Ensifer americanum CFNEI 156T", "gbrs_paired_asm": "GCA_001651855.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/651/855/GCF_001651855.1_ASM165185v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6653547", "genome_size_ungapped": "6653547", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "82", "contig_count": "82", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-26", "total_gene_count": "6256", "protein_coding_gene_count": "6038", "non_coding_gene_count": "54", "pubmed_id": "27125987" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-05-25", "dateModified": "2016-05-25", "datePublished": "2016-05-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Sinorhizobium americanum" ], "sample_taxid": [ "194963" ], "sample_host_organism": [ "Acacia" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Mexico" ], "sample_host_location_id": [], "data_size": "1.861 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)": "6653547", "Number of Sequences": "82", "Longest Sequences (bp)": "428321", "N50 (bp)": "207808", "Gap Ratio (%)": "0.000286", "GCcontent (%)": "62.3", "Number of CDSs": "6221", "Average Protein Length": "307.7", "Coding Ratio (%)": "86.3", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sinorhizobium fredii", "strain": "strain=NBRC 14780", "accession": "GCA_006539605.1", "taxid": 380, "species_taxid": 380, "relation_to_type": "type", "validated": true, "ani": 88.2303, "matched_fragments": 1513, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium fredii", "strain": "strain=USDA 205", "accession": "GCA_001461695.1", "taxid": 380, "species_taxid": 380, "relation_to_type": "type", "validated": true, "ani": 88.1573, "matched_fragments": 1550, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium fredii", "strain": "strain=USDA205", "accession": "GCA_009601405.1", "taxid": 380, "species_taxid": 380, "relation_to_type": "type", "validated": true, "ani": 88.1043, "matched_fragments": 1576, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer sojae", "strain": "strain=CCBAU 05684", "accession": "GCA_000261485.1", "taxid": 716925, "species_taxid": 716925, "relation_to_type": "type", "validated": true, "ani": 83.0314, "matched_fragments": 1157, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer sojae", "strain": "strain=CCBAU 05684", "accession": "GCA_002288525.1", "taxid": 716925, "species_taxid": 716925, "relation_to_type": "type", "validated": true, "ani": 83.0311, "matched_fragments": 1211, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium kostiense", "strain": "strain=DSM 13372", "accession": "GCA_017874595.1", "taxid": 76747, "species_taxid": 76747, "relation_to_type": "type", "validated": true, "ani": 82.9169, "matched_fragments": 1290, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer alkalisoli", "strain": "strain=YIC4027", "accession": "GCA_001723275.1", "taxid": 1752398, "species_taxid": 1752398, "relation_to_type": "type", "validated": true, "ani": 82.8735, "matched_fragments": 1203, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer alkalisoli", "strain": "strain=YIC4027", "accession": "GCA_008932245.1", "taxid": 1752398, "species_taxid": 1752398, "relation_to_type": "type", "validated": true, "ani": 82.8195, "matched_fragments": 1220, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer mexicanus", "strain": "strain=ITTG R7", "accession": "GCA_013488225.1", "taxid": 375549, "species_taxid": 375549, "relation_to_type": "type", "validated": true, "ani": 82.7978, "matched_fragments": 1280, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer psoraleae", "strain": "strain=CCBAU 65732", "accession": "GCA_013283645.1", "taxid": 520838, "species_taxid": 520838, "relation_to_type": "type", "validated": true, "ani": 82.7564, "matched_fragments": 1262, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer mexicanus", "strain": "strain=DSM 18446", "accession": "GCA_017873105.1", "taxid": 375549, "species_taxid": 375549, "relation_to_type": "type", "validated": true, "ani": 82.7227, "matched_fragments": 1280, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium arboris", "strain": "strain=LMG 14919", "accession": "GCA_000427465.1", "taxid": 76745, "species_taxid": 76745, "relation_to_type": "type", "validated": true, "ani": 82.5195, "matched_fragments": 1258, "total_fragments": 2176, "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": 81.1402, "matched_fragments": 803, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella yambaruensis", "strain": "strain=DSM 18801", "accession": "GCA_022899355.1", "taxid": 415996, "species_taxid": 415996, "relation_to_type": "type", "validated": true, "ani": 80.7965, "matched_fragments": 914, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella zoogloeoides", "strain": "strain=ATCC 19623", "accession": "GCA_020883495.1", "taxid": 352475, "species_taxid": 352475, "relation_to_type": "type", "validated": true, "ani": 80.64, "matched_fragments": 742, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella sumterensis", "strain": "strain=MEC087", "accession": "GCA_004514425.2", "taxid": 1967501, "species_taxid": 1967501, "relation_to_type": "type", "validated": true, "ani": 80.2102, "matched_fragments": 739, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella oryzae", "strain": "strain=Z-25", "accession": "GCA_023038235.1", "taxid": 2871820, "species_taxid": 2871820, "relation_to_type": "type", "validated": true, "ani": 80.1376, "matched_fragments": 731, "total_fragments": 2176, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001651855.1", "gtdb_species": "s__Sinorhizobium americanum", "ani": 100.0, "matched_fragments": 2173, "total_fragments": 2176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.12", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_002944405.1", "gtdb_species": "s__Sinorhizobium fredii_C", "ani": 93.0747, "matched_fragments": 1757, "total_fragments": 2176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "98.35", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000378985.1", "gtdb_species": "s__Sinorhizobium sp000378985", "ani": 89.199, "matched_fragments": 1690, "total_fragments": 2176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_001651865.1", "gtdb_species": "s__Sinorhizobium glycinis", "ani": 88.4421, "matched_fragments": 1489, "total_fragments": 2176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_000018545.1", "gtdb_species": "s__Sinorhizobium fredii_A", "ani": 88.1798, "matched_fragments": 1594, "total_fragments": 2176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_001461695.1", "gtdb_species": "s__Sinorhizobium fredii", "ani": 88.1573, "matched_fragments": 1550, "total_fragments": 2176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "96.82", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_000265205.3", "gtdb_species": "s__Sinorhizobium fredii_B", "ani": 87.9341, "matched_fragments": 1624, "total_fragments": 2176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_001704765.1", "gtdb_species": "s__Sinorhizobium shofinae", "ani": 87.6384, "matched_fragments": 1322, "total_fragments": 2176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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": 0.176, "growth_tmp": 30.0, "optimum_tmp": 30.0, "optimum_ph": null, "genome_size": 6665737.273, "gc_content": 61.302, "coding_genes": 6110.0, "rRNA16S_genes": 3.0, "tRNA_genes": 54.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.5, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Sinorhizobium", "americanum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }