{ "type": "genome", "identifier": "GCA_028287385.1", "organism": "Gemmatimonadota bacterium", "title": "Gemmatimonadota bacterium", "description": "derived from metagenome; fragmented assembly; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Colorado State University", "publication": [ {} ], "properties": { "assembly_accession": "GCA_028287385.1", "bioproject": "PRJNA682830", "biosample": "SAMN17837442", "wgs_master": "JAQBPT000000000.1", "refseq_category": "na", "taxid": "2026742", "species_taxid": "2026742", "organism_name": "Gemmatimonadota bacterium", "infraspecific_name": "", "isolate": "RYN_354", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/01/30", "asm_name": "ASM2828738v1", "submitter": "Colorado State University", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/287/385/GCA_028287385.1_ASM2828738v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-01-30", "dateModified": "2023-01-30", "datePublished": "2023-01-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Gemmatimonadota bacterium" ], "sample_taxid": [ "2026742" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA:Wyoming" ], "sample_host_location_id": [], "data_size": "0.653 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 53.12, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2366419", "Number of Sequences": "536", "Longest Sequences (bp)": "13449", "N50 (bp)": "4564", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.6", "Number of CDSs": "1674", "Average Protein Length": "295.8", "Coding Ratio (%)": "62.8", "Number of rRNAs": "0", "Number of tRNAs": "11", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Burkholderia glumae", "strain": "strain=LMG 2196", "accession": "GCA_902832765.1", "taxid": 337, "species_taxid": 337, "relation_to_type": "type", "validated": true, "ani": 74.6993, "matched_fragments": 60, "total_fragments": 527, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis tolypomycina", "strain": "strain=DSM 44544", "accession": "GCA_900105945.1", "taxid": 208445, "species_taxid": 208445, "relation_to_type": "type", "validated": true, "ani": 74.6267, "matched_fragments": 69, "total_fragments": 527, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vastitatis", "strain": "strain=H5", "accession": "GCA_002234595.1", "taxid": 1905142, "species_taxid": 1905142, "relation_to_type": "type", "validated": true, "ani": 74.5662, "matched_fragments": 59, "total_fragments": 527, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 53.12, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_013361335.1", "gtdb_species": "s__AG11 sp013361335", "ani": 79.5525, "matched_fragments": 252, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.60", "min_intra_species_ani": "99.48", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_003223455.1", "gtdb_species": "s__AG11 sp003223455", "ani": 78.2017, "matched_fragments": 227, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11", "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": "GCA_002215645.1", "gtdb_species": "s__AG11 sp002215645", "ani": 77.3391, "matched_fragments": 149, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11", "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": "GCA_014378185.1", "gtdb_species": "s__AG11 sp014378185", "ani": 77.3078, "matched_fragments": 122, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11", "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": "GCA_013361935.1", "gtdb_species": "s__JABFXC01 sp013361935", "ani": 76.7989, "matched_fragments": 140, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.88", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_013361745.1", "gtdb_species": "s__JABFXC01 sp013361745", "ani": 76.7965, "matched_fragments": 96, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01", "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": "GCA_016194585.1", "gtdb_species": "s__Fen-1231 sp016194585", "ani": 76.5862, "matched_fragments": 100, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "99.33", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013820975.1", "gtdb_species": "s__JACDHQ01 sp013820975", "ani": 76.5848, "matched_fragments": 64, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACDHQ01", "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": "GCA_902825965.1", "gtdb_species": "s__PNKF01 sp902825965", "ani": 76.1403, "matched_fragments": 79, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01", "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": "GCA_013697785.1", "gtdb_species": "s__FEN-1250 sp013697785", "ani": 75.9205, "matched_fragments": 65, "total_fragments": 527, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__FEN-1250", "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": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Gemmatimonadota", "c__Gemmatimonadetes", "o__Gemmatimonadales", "f__Gemmatimonadaceae", "g__AG11", "s__" ], "_genome_taxon": [ "Gemmatimonadota", "bacterium", "d__Bacteria", "p__Gemmatimonadota", "c__Gemmatimonadetes", "o__Gemmatimonadales", "f__Gemmatimonadaceae", "g__AG11", "s__", "Bacteria", "Gemmatimonadota", "Gemmatimonadetes", "Gemmatimonadales", "Gemmatimonadaceae", "AG11", "s", "", "" ], "_meo": [ { "id": "MEO_0000007", "label": "soil" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }