{ "type": "genome", "identifier": "GCF_900167305.1", "organism": "Garciella nitratireducens DSM 15102", "title": "Garciella nitratireducens DSM 15102", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900167305.1", "bioproject": "PRJNA224116", "biosample": "SAMN02745973", "wgs_master": "FUWV00000000.1", "refseq_category": "reference genome", "taxid": "1121911", "species_taxid": "218205", "organism_name": "Garciella nitratireducens DSM 15102", "infraspecific_name": "strain=DSM 15102", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/03/04", "asm_name": "IMG-taxon 2568526006 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900167305.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/167/305/GCF_900167305.1_IMG-taxon_2568526006_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2163332", "genome_size_ungapped": "2160837", "gc_percent": "30.500000", "replicon_count": "0", "scaffold_count": "26", "contig_count": "26", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900167305.1-RS_2024_04_12", "annotation_date": "2024-04-12", "total_gene_count": "2216", "protein_coding_gene_count": "2100", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-03-04", "dateModified": "2017-03-04", "datePublished": "2017-03-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Garciella nitratireducens DSM 15102" ], "sample_taxid": [ "1121911" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Mexico:SAMIII oilfield, Tabasco, Gulf of Mexico" ], "sample_host_location_id": [], "data_size": "0.592 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2163332", "Number of Sequences": "26", "Longest Sequences (bp)": "428663", "N50 (bp)": "143239", "Gap Ratio (%)": "0.115331", "GCcontent (%)": "30.4", "Number of CDSs": "2129", "Average Protein Length": "295.7", "Coding Ratio (%)": "87.3", "Number of rRNAs": "7", "Number of tRNAs": "64", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Garciella nitratireducens", "strain": "strain=DSM 15102", "accession": "GCA_900167305.1", "taxid": 218205, "species_taxid": 218205, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 704, "total_fragments": 708, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Irregularibacter muris", "strain": "strain=DSM 28593", "accession": "GCA_024622505.1", "taxid": 1796619, "species_taxid": 1796619, "relation_to_type": "type", "validated": true, "ani": 76.7893, "matched_fragments": 96, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium aciditolerans", "strain": "strain=DSM 17425", "accession": "GCA_016316925.1", "taxid": 339861, "species_taxid": 339861, "relation_to_type": "type", "validated": true, "ani": 76.481, "matched_fragments": 55, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidibacter thalassicus", "strain": "strain=DSM 15285", "accession": "GCA_900129915.1", "taxid": 214905, "species_taxid": 214905, "relation_to_type": "type", "validated": true, "ani": 75.9069, "matched_fragments": 58, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crassaminicella profunda", "strain": "strain=Ra1766H", "accession": "GCA_019884785.1", "taxid": 1286698, "species_taxid": 1286698, "relation_to_type": "type", "validated": true, "ani": 75.8147, "matched_fragments": 87, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaeromonas gelatinilytica", "strain": "strain=D2Q-14", "accession": "GCA_016820635.1", "taxid": 2683194, "species_taxid": 2683194, "relation_to_type": "type", "validated": true, "ani": 75.5193, "matched_fragments": 81, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium arbusti", "strain": "strain=SL206", "accession": "GCA_000246895.2", "taxid": 1137848, "species_taxid": 1137848, "relation_to_type": "type", "validated": true, "ani": 74.8723, "matched_fragments": 54, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900167305.1", "gtdb_species": "s__Garciella nitratireducens", "ani": 100.0, "matched_fragments": 704, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Garciellaceae;g__Garciella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.29", "min_intra_species_ani": "99.29", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCA_900555725.1", "gtdb_species": "s__Garciella sp900555725", "ani": 80.681, "matched_fragments": 309, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Garciellaceae;g__Garciella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009696605.1", "gtdb_species": "s__Anaerosalibacter bizertensis", "ani": 77.4992, "matched_fragments": 52, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "98.48", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_019203185.1", "gtdb_species": "s__143-21 sp019203185", "ani": 76.0506, "matched_fragments": 77, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__143-21", "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_016820635.1", "gtdb_species": "s__Senegalia sp016820635", "ani": 75.5325, "matched_fragments": 80, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia", "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_017100085.1", "gtdb_species": "s__Clostridium_H botulinum_A", "ani": 75.1016, "matched_fragments": 55, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0162, "mean_intra_species_ani": "99.30", "min_intra_species_ani": "99.03", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_000246895.1", "gtdb_species": "s__Clostridium_I arbusti", "ani": 74.8724, "matched_fragments": 54, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I", "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": -0.302, "cell_length": 0.146, "doubling_h": null, "growth_tmp": 55.0, "optimum_tmp": 55.0, "optimum_ph": null, "genome_size": 2163332.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 1.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Garciella", "nitratireducens", "DSM", "15102" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }