{ "type": "genome", "identifier": "GCA_013822035.1", "organism": "Gemmatimonas sp.", "title": "Gemmatimonas sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Illinois at Urbana-Champaign", "publication": [ {} ], "properties": { "assembly_accession": "GCA_013822035.1", "bioproject": "PRJNA323575", "biosample": "SAMN08286422", "wgs_master": "PNJS00000000.1", "refseq_category": "na", "taxid": "1962908", "species_taxid": "1962908", "organism_name": "Gemmatimonas sp.", "infraspecific_name": "", "isolate": "WM.3.45", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/28", "asm_name": "ASM1382203v1", "submitter": "University of Illinois at Urbana-Champaign", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/822/035/GCA_013822035.1_ASM1382203v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-07-28", "dateModified": "2020-07-28", "datePublished": "2020-07-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Gemmatimonas sp." ], "sample_taxid": [ "1962908" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Illinois, Champaign" ], "sample_host_location_id": [], "data_size": "1.052 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": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3791484", "Number of Sequences": "83", "Longest Sequences (bp)": "213928", "N50 (bp)": "71073", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.0", "Number of CDSs": "3246", "Average Protein Length": "355.7", "Coding Ratio (%)": "91.4", "Number of rRNAs": "0", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gemmatimonas aurantiaca", "strain": "strain=T-27", "accession": "GCA_000010305.1", "taxid": 173480, "species_taxid": 173480, "relation_to_type": "type", "validated": true, "ani": 79.3499, "matched_fragments": 521, "total_fragments": 1224, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmatimonas phototrophica", "strain": "strain=AP64", "accession": "GCA_000695095.2", "taxid": 1379270, "species_taxid": 1379270, "relation_to_type": "type", "validated": true, "ani": 79.1272, "matched_fragments": 523, "total_fragments": 1224, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmatimonas groenlandica", "strain": "strain=TET16", "accession": "GCA_013004105.1", "taxid": 2732249, "species_taxid": 2732249, "relation_to_type": "type", "validated": true, "ani": 78.4648, "matched_fragments": 461, "total_fragments": 1224, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmatirosa kalamazoonensis", "strain": "strain=KBS708", "accession": "GCA_000522985.1", "taxid": 861299, "species_taxid": 861299, "relation_to_type": "type", "validated": true, "ani": 76.7552, "matched_fragments": 241, "total_fragments": 1224, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Longimicrobium terrae", "strain": "strain=DSM 29007", "accession": "GCA_014202995.1", "taxid": 1639882, "species_taxid": 1639882, "relation_to_type": "type", "validated": true, "ani": 75.4856, "matched_fragments": 115, "total_fragments": 1224, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Longimicrobium terrae", "strain": "strain=CB-286315", "accession": "GCA_013000925.1", "taxid": 1639882, "species_taxid": 1639882, "relation_to_type": "type", "validated": true, "ani": 75.4727, "matched_fragments": 119, "total_fragments": 1224, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dokdonella fugitiva", "strain": "strain=A3", "accession": "GCA_004342425.1", "taxid": 328517, "species_taxid": 328517, "relation_to_type": "type", "validated": true, "ani": 75.0117, "matched_fragments": 55, "total_fragments": 1224, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_002483225.1", "gtdb_species": "s__Gemmatimonas sp002483225", "ani": 97.6982, "matched_fragments": 1170, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.70", "min_intra_species_ani": "97.70", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_016741895.1", "gtdb_species": "s__Gemmatimonas sp016741895", "ani": 89.6813, "matched_fragments": 908, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas", "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_016742275.1", "gtdb_species": "s__Gemmatimonas sp016742275", "ani": 80.5242, "matched_fragments": 700, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas", "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_000010305.1", "gtdb_species": "s__Gemmatimonas aurantiaca", "ani": 79.3448, "matched_fragments": 521, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas", "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_000695095.2", "gtdb_species": "s__Gemmatimonas phototrophica", "ani": 79.1272, "matched_fragments": 523, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas", "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_013004105.1", "gtdb_species": "s__Gemmatimonas sp013004105", "ani": 78.456, "matched_fragments": 462, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas", "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_011390885.1", "gtdb_species": "s__JAABRT01 sp011390885", "ani": 78.2574, "matched_fragments": 380, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JAABRT01", "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_016720905.1", "gtdb_species": "s__Gemmatimonas sp016720905", "ani": 77.6891, "matched_fragments": 322, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas", "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_014377535.1", "gtdb_species": "s__JACMLX01 sp014377535", "ani": 76.6443, "matched_fragments": 139, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACMLX01", "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_003152485.1", "gtdb_species": "s__Palsa-1248 sp003152485", "ani": 76.2469, "matched_fragments": 75, "total_fragments": 1224, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Palsa-1248", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.76", "min_intra_species_ani": "99.74", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.155, "cell_length": null, "doubling_h": 1.079, "growth_tmp": 30.0, "optimum_tmp": 27.5, "optimum_ph": null, "genome_size": 4675788.9, "gc_content": 64.349, "coding_genes": 3820.5, "rRNA16S_genes": 1.5, "tRNA_genes": 47.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Gemmatimonadota", "c__Gemmatimonadetes", "o__Gemmatimonadales", "f__Gemmatimonadaceae", "g__Gemmatimonas", "s__Gemmatimonas sp002483225" ], "_genome_taxon": [ "Gemmatimonas", "sp.", "d__Bacteria", "p__Gemmatimonadota", "c__Gemmatimonadetes", "o__Gemmatimonadales", "f__Gemmatimonadaceae", "g__Gemmatimonas", "s__Gemmatimonas sp002483225", "Bacteria", "Gemmatimonadota", "Gemmatimonadetes", "Gemmatimonadales", "Gemmatimonadaceae", "Gemmatimonas", "Gemmatimonas", "sp002483225" ], "_meo": [ { "id": "MEO_0000907", "label": "drinking water" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }