{ "type": "genome", "identifier": "GCF_003628305.1", "organism": "Cohnella endophytica", "title": "Cohnella endophytica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Center for Medicine & Biology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003628305.1", "bioproject": "PRJNA224116", "biosample": "SAMN10145370", "wgs_master": "RBZM00000000.1", "refseq_category": "reference genome", "taxid": "2419778", "species_taxid": "2419778", "organism_name": "Cohnella endophytica", "infraspecific_name": "strain=M2MS4P-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/11", "asm_name": "ASM362830v1", "asm_submitter": "Research Center for Medicine & Biology", "gbrs_paired_asm": "GCA_003628305.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/628/305/GCF_003628305.1_ASM362830v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6268162", "genome_size_ungapped": "6268162", "gc_percent": "51.500000", "replicon_count": "0", "scaffold_count": "32", "contig_count": "32", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003628305.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "5411", "protein_coding_gene_count": "5286", "non_coding_gene_count": "89", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-11", "dateModified": "2018-10-11", "datePublished": "2018-10-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Cohnella endophytica" ], "sample_taxid": [ "2419778" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Guangxi" ], "sample_host_location_id": [], "data_size": "1.774 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)": "6268162", "Number of Sequences": "32", "Longest Sequences (bp)": "925366", "N50 (bp)": "501394", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "51.5", "Number of CDSs": "5406", "Average Protein Length": "342.8", "Coding Ratio (%)": "88.7", "Number of rRNAs": "4", "Number of tRNAs": "65", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cohnella endophytica", "strain": "strain=M2MS4P-1", "accession": "GCA_003628305.1", "taxid": 2419778, "species_taxid": 2419778, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2075, "total_fragments": 2076, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cohnella herbarum", "strain": "strain=MFER-1", "accession": "GCA_012849095.1", "taxid": 2728023, "species_taxid": 2728023, "relation_to_type": "type", "validated": true, "ani": 79.916, "matched_fragments": 721, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cohnella luojiensis", "strain": "strain=CCTCC AB 208254", "accession": "GCA_004564235.1", "taxid": 652876, "species_taxid": 652876, "relation_to_type": "type", "validated": true, "ani": 79.7297, "matched_fragments": 565, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cohnella cholangitidis", "strain": "strain=1605-214", "accession": "GCA_014107495.1", "taxid": 2598458, "species_taxid": 2598458, "relation_to_type": "type", "validated": true, "ani": 79.5849, "matched_fragments": 640, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cohnella lupini", "strain": "strain=CECT 8236", "accession": "GCA_003386205.1", "taxid": 1294267, "species_taxid": 1294267, "relation_to_type": "type", "validated": true, "ani": 79.5379, "matched_fragments": 649, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cohnella terricola", "strain": "strain=G13", "accession": "GCA_007786475.1", "taxid": 1289167, "species_taxid": 1289167, "relation_to_type": "type", "validated": true, "ani": 79.2635, "matched_fragments": 556, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cohnella panacarvi", "strain": "strain=Gsoil 349", "accession": "GCA_000515335.1", "taxid": 400776, "species_taxid": 400776, "relation_to_type": "type", "validated": true, "ani": 78.1553, "matched_fragments": 392, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cohnella xylanilytica", "strain": "strain=DSM 25239", "accession": "GCA_014212175.1", "taxid": 557555, "species_taxid": 557555, "relation_to_type": "type", "validated": true, "ani": 77.1286, "matched_fragments": 328, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus agri", "strain": "strain=JW14", "accession": "GCA_013359945.1", "taxid": 2744309, "species_taxid": 2744309, "relation_to_type": "type", "validated": true, "ani": 77.0996, "matched_fragments": 65, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cohnella lubricantis", "strain": "strain=DSM 103658", "accession": "GCA_014212015.1", "taxid": 2163172, "species_taxid": 2163172, "relation_to_type": "type", "validated": true, "ani": 77.0258, "matched_fragments": 231, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cohnella lubricantis", "strain": "strain=DSM 103658", "accession": "GCA_017874835.1", "taxid": 2163172, "species_taxid": 2163172, "relation_to_type": "type", "validated": true, "ani": 77.018, "matched_fragments": 233, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus artemisiicola", "strain": "strain=MWE-103", "accession": "GCA_017652985.1", "taxid": 1172618, "species_taxid": 1172618, "relation_to_type": "type", "validated": true, "ani": 76.5186, "matched_fragments": 229, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus rhizophilus", "strain": "strain=7197", "accession": "GCA_003854965.1", "taxid": 1850366, "species_taxid": 1850366, "relation_to_type": "type", "validated": true, "ani": 76.3878, "matched_fragments": 91, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus macerans", "strain": "strain=ATCC 8244", "accession": "GCA_000746875.1", "taxid": 44252, "species_taxid": 44252, "relation_to_type": "type", "validated": true, "ani": 76.3125, "matched_fragments": 113, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003628305.1", "gtdb_species": "s__Cohnella endophytica", "ani": 100.0, "matched_fragments": 2075, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella", "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_017874175.1", "gtdb_species": "s__Cohnella suwonensis", "ani": 79.9305, "matched_fragments": 687, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella", "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_012849095.1", "gtdb_species": "s__Cohnella sp012849095", "ani": 79.9141, "matched_fragments": 719, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella", "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_004564235.1", "gtdb_species": "s__Cohnella luojiensis", "ani": 79.7252, "matched_fragments": 566, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella", "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_003386205.1", "gtdb_species": "s__Cohnella lupini", "ani": 79.5324, "matched_fragments": 650, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella", "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_007786475.1", "gtdb_species": "s__Cohnella terricola", "ani": 79.2703, "matched_fragments": 556, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella", "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_003001675.1", "gtdb_species": "s__Cohnella sp003001675", "ani": 78.6572, "matched_fragments": 581, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003386235.1", "gtdb_species": "s__Cohnella phaseoli", "ani": 78.3227, "matched_fragments": 471, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.76", "min_intra_species_ani": "97.76", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000515335.1", "gtdb_species": "s__Cohnella panacarvi", "ani": 78.1489, "matched_fragments": 393, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella", "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": -0.356, "cell_length": 0.316, "doubling_h": null, "growth_tmp": 31.421, "optimum_tmp": 31.714, "optimum_ph": 6.923, "genome_size": 4660270.0, "gc_content": 55.152, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.8, "range_salinity": null, "facultative_respiration": 0.235, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.764, "mesophilic_range_tmp": 0.5, "thermophilic_range_tmp": 0.5, "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": [ "Cohnella", "endophytica" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }