{ "type": "genome", "identifier": "GCF_900167555.1", "organism": "Gemmiger formicilis", "title": "Gemmiger formicilis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900167555.1", "bioproject": "PRJNA224116", "biosample": "SAMN02745178", "wgs_master": "FUYF00000000.1", "refseq_category": "reference genome", "taxid": "745368", "species_taxid": "745368", "organism_name": "Gemmiger formicilis", "infraspecific_name": "strain=ATCC 27749", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/03/04", "asm_name": "IMG-taxon 2590828806 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900167555.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/167/555/GCF_900167555.1_IMG-taxon_2590828806_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": "3241569", "genome_size_ungapped": "3241549", "gc_percent": "58.000000", "replicon_count": "0", "scaffold_count": "92", "contig_count": "92", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900167555.1-RS_2024_03_30", "annotation_date": "2024-03-30", "total_gene_count": "2969", "protein_coding_gene_count": "2855", "non_coding_gene_count": "62", "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": [ "Gemmiger formicilis" ], "sample_taxid": [ "745368" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.911 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)": "3241569", "Number of Sequences": "92", "Longest Sequences (bp)": "375470", "N50 (bp)": "185679", "Gap Ratio (%)": "0.000617", "GCcontent (%)": "58.1", "Number of CDSs": "2876", "Average Protein Length": "318.9", "Coding Ratio (%)": "84.9", "Number of rRNAs": "2", "Number of tRNAs": "57", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Subdoligranulum variabile", "strain": "strain=DSM 15176", "accession": "GCA_000157955.1", "taxid": 214851, "species_taxid": 214851, "relation_to_type": "type", "validated": true, "ani": 81.1943, "matched_fragments": 398, "total_fragments": 1033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Subdoligranulum variabile", "strain": "strain=DSM 15176", "accession": "GCA_025152575.1", "taxid": 214851, "species_taxid": 214851, "relation_to_type": "type", "validated": true, "ani": 81.1373, "matched_fragments": 415, "total_fragments": 1033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalibacterium duncaniae", "strain": "strain=JCM 31915", "accession": "GCA_010509575.1", "taxid": 411483, "species_taxid": 411483, "relation_to_type": "type", "validated": true, "ani": 80.3531, "matched_fragments": 283, "total_fragments": 1033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalibacterium duncaniae", "strain": "strain=A2-165", "accession": "GCA_000162015.1", "taxid": 411483, "species_taxid": 411483, "relation_to_type": "type", "validated": true, "ani": 80.1755, "matched_fragments": 282, "total_fragments": 1033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalibacterium hattorii", "strain": "strain=APC922/41-1", "accession": "GCA_003287455.1", "taxid": 2935520, "species_taxid": 2935520, "relation_to_type": "type", "validated": true, "ani": 80.0003, "matched_fragments": 290, "total_fragments": 1033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fournierella massiliensis", "strain": "strain=DSM 100451", "accession": "GCA_004345265.1", "taxid": 1650663, "species_taxid": 1650663, "relation_to_type": "type", "validated": true, "ani": 79.1583, "matched_fragments": 197, "total_fragments": 1033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalibacterium gallinarum", "strain": "strain=JCM 17207", "accession": "GCA_022180365.1", "taxid": 2903556, "species_taxid": 2903556, "relation_to_type": "type", "validated": true, "ani": 78.8899, "matched_fragments": 198, "total_fragments": 1033, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900167555.1", "gtdb_species": "s__Gemmiger formicilis", "ani": 100.0, "matched_fragments": 1023, "total_fragments": 1033, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.67", "min_intra_species_ani": "96.73", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.78", "num_clustered_genomes": 43, "status": "conclusive" }, { "accession": "GCF_018784445.1", "gtdb_species": "s__Gemmiger sp900540775", "ani": 88.0061, "matched_fragments": 778, "total_fragments": 1033, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.04", "min_intra_species_ani": "97.97", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.81", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_900540595.1", "gtdb_species": "s__Gemmiger sp900540595", "ani": 87.6373, "matched_fragments": 661, "total_fragments": 1033, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.09", "min_intra_species_ani": "95.97", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_900554145.1", "gtdb_species": "s__Gemmiger sp900554145", "ani": 85.7421, "matched_fragments": 497, "total_fragments": 1033, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.15", "min_intra_species_ani": "98.15", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.80", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_004554775.1", "gtdb_species": "s__Gemmiger variabilis_B", "ani": 83.9324, "matched_fragments": 598, "total_fragments": 1033, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.40", "min_intra_species_ani": "97.89", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900539695.1", "gtdb_species": "s__Gemmiger sp900539695", "ani": 83.6765, "matched_fragments": 540, "total_fragments": 1033, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "97.91", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.79", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_004552305.1", "gtdb_species": "s__Gemmiger variabilis_A", "ani": 82.0334, "matched_fragments": 421, "total_fragments": 1033, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.82", "min_intra_species_ani": "96.59", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.70", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_003343905.1", "gtdb_species": "s__Gemmiger variabilis_C", "ani": 80.8682, "matched_fragments": 419, "total_fragments": 1033, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger", "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": -0.523, "cell_length": -0.523, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 3241569.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "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": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Gemmiger", "formicilis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }