{ "type": "genome", "identifier": "GCF_003367905.1", "organism": "Megasphaera stantonii", "title": "Megasphaera stantonii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "USDA ARS", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003367905.1", "bioproject": "PRJNA224116", "biosample": "SAMN09213727", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2144175", "species_taxid": "2144175", "organism_name": "Megasphaera stantonii", "infraspecific_name": "strain=AJH120", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/09", "asm_name": "ASM336790v1", "asm_submitter": "USDA ARS", "gbrs_paired_asm": "GCA_003367905.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/367/905/GCF_003367905.1_ASM336790v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2652760", "genome_size_ungapped": "2652760", "gc_percent": "52.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003367905.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2511", "protein_coding_gene_count": "2411", "non_coding_gene_count": "79", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-09", "dateModified": "2018-08-09", "datePublished": "2018-08-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Megasphaera stantonii" ], "sample_taxid": [ "2144175" ], "sample_host_organism": [ "Gallus gallus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Iowa" ], "sample_host_location_id": [], "data_size": "0.744 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)": "2652760", "Number of Sequences": "1", "Longest Sequences (bp)": "2652760", "N50 (bp)": "2652760", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.6", "Number of CDSs": "2447", "Average Protein Length": "317.1", "Coding Ratio (%)": "87.7", "Number of rRNAs": "18", "Number of tRNAs": "57", "Number of CRISPRs": "6" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Megasphaera stantonii", "strain": "strain=AJH120", "accession": "GCA_003367905.1", "taxid": 2144175, "species_taxid": 2144175, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 884, "total_fragments": 884, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Megasphaera stantonii", "strain": "strain=AJH120", "accession": "GCA_003030445.1", "taxid": 2144175, "species_taxid": 2144175, "relation_to_type": "type", "validated": true, "ani": 99.9432, "matched_fragments": 827, "total_fragments": 884, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Megasphaera elsdenii", "strain": "strain=DSM 20460", "accession": "GCA_000283495.2", "taxid": 907, "species_taxid": 907, "relation_to_type": "type", "validated": true, "ani": 79.9768, "matched_fragments": 348, "total_fragments": 884, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Megasphaera elsdenii", "strain": "strain=ATCC 25940", "accession": "GCA_003010495.1", "taxid": 907, "species_taxid": 907, "relation_to_type": "type", "validated": true, "ani": 79.9533, "matched_fragments": 344, "total_fragments": 884, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Megasphaera massiliensis", "strain": "strain=NP3", "accession": "GCA_000455225.1", "taxid": 1232428, "species_taxid": 1232428, "relation_to_type": "suspected-type", "validated": true, "ani": 78.8644, "matched_fragments": 287, "total_fragments": 884, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Megasphaera cerevisiae", "strain": "strain=DSM 20462", "accession": "GCA_001045675.1", "taxid": 39029, "species_taxid": 39029, "relation_to_type": "type", "validated": true, "ani": 77.5802, "matched_fragments": 166, "total_fragments": 884, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mitsuokella jalaludinii", "strain": "strain=DSM 13811", "accession": "GCA_000702905.1", "taxid": 187979, "species_taxid": 187979, "relation_to_type": "type", "validated": true, "ani": 76.7232, "matched_fragments": 51, "total_fragments": 884, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003367905.1", "gtdb_species": "s__Megasphaera stantonii", "ani": 100.0, "matched_fragments": 884, "total_fragments": 884, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.46", "min_intra_species_ani": "96.44", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCA_900554215.1", "gtdb_species": "s__Megasphaera sp900554215", "ani": 94.7466, "matched_fragments": 538, "total_fragments": 884, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.76", "min_intra_species_ani": "95.76", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000417505.1", "gtdb_species": "s__Megasphaera sp000417505", "ani": 80.0646, "matched_fragments": 356, "total_fragments": 884, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.18", "min_intra_species_ani": "97.65", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.81", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_003010495.1", "gtdb_species": "s__Megasphaera elsdenii", "ani": 79.8746, "matched_fragments": 343, "total_fragments": 884, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "97.55", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.81", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCA_902388315.1", "gtdb_species": "s__Megasphaera sp902388315", "ani": 79.7006, "matched_fragments": 257, "total_fragments": 884, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.43", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900548635.1", "gtdb_species": "s__Megasphaera sp900548635", "ani": 79.5649, "matched_fragments": 269, "total_fragments": 884, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.28", "min_intra_species_ani": "98.56", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.79", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001546855.1", "gtdb_species": "s__Megasphaera sp001546855", "ani": 79.03, "matched_fragments": 290, "total_fragments": 884, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 9, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.079, "cell_length": 0.123, "doubling_h": null, "growth_tmp": 33.166, "optimum_tmp": 34.28, "optimum_ph": 7.0, "genome_size": 2655872.984, "gc_content": 49.092, "coding_genes": 2438.25, "rRNA16S_genes": 7.0, "tRNA_genes": 58.666, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Megasphaera", "stantonii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }