{ "type": "genome", "identifier": "GCA_022756045.1", "organism": "Limosilactobacillus vaginalis", "title": "Limosilactobacillus vaginalis", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Massachusetts General Hospital", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022756045.1", "bioproject": "PRJNA799762", "biosample": "SAMN25208438", "wgs_master": "JALBTH000000000.1", "refseq_category": "na", "taxid": "1633", "species_taxid": "1633", "organism_name": "Limosilactobacillus vaginalis", "infraspecific_name": "", "isolate": "MHKL_MAG_00319", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/03/29", "asm_name": "ASM2275604v1", "submitter": "Massachusetts General Hospital", "gbrs_paired_asm": "GCF_022756045.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/756/045/GCA_022756045.1_ASM2275604v1", "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": "2022-03-29", "dateModified": "2022-03-29", "datePublished": "2022-03-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Limosilactobacillus vaginalis" ], "sample_taxid": [ "1633" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.496 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)": "1732606", "Number of Sequences": "138", "Longest Sequences (bp)": "169663", "N50 (bp)": "17832", "Gap Ratio (%)": "0.002886", "GCcontent (%)": "40.4", "Number of CDSs": "1654", "Average Protein Length": "290.5", "Coding Ratio (%)": "83.2", "Number of rRNAs": "0", "Number of tRNAs": "32", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Limosilactobacillus vaginalis", "strain": "strain=DSM 5837", "accession": "GCA_001435915.1", "taxid": 1633, "species_taxid": 1633, "relation_to_type": "type", "validated": true, "ani": 98.8479, "matched_fragments": 424, "total_fragments": 511, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Limosilactobacillus vaginalis", "strain": "strain=ATCC 49540", "accession": "GCA_000159435.1", "taxid": 1633, "species_taxid": 1633, "relation_to_type": "type", "validated": true, "ani": 98.8077, "matched_fragments": 465, "total_fragments": 511, "ani_threshold": 95, "status": 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"organism_name": "Limosilactobacillus frumenti", "strain": "strain=DSM 13145", "accession": "GCA_001436045.1", "taxid": 104955, "species_taxid": 104955, "relation_to_type": "type", "validated": true, "ani": 79.5972, "matched_fragments": 187, "total_fragments": 511, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000159435.1", "gtdb_species": "s__Limosilactobacillus vaginalis", "ani": 98.8077, "matched_fragments": 465, "total_fragments": 511, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "96.39", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.86", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCF_014838735.1", "gtdb_species": "s__Limosilactobacillus 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83.9519, "matched_fragments": 338, "total_fragments": 511, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "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_014145505.1", "gtdb_species": "s__Limosilactobacillus fastidiosus", "ani": 82.5861, "matched_fragments": 311, "total_fragments": 511, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.58", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018883805.1", "gtdb_species": "s__Limosilactobacillus merdavium", "ani": 82.0455, "matched_fragments": 261, "total_fragments": 511, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.07", "min_intra_species_ani": "96.07", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001436045.1", "gtdb_species": "s__Limosilactobacillus frumenti", "ani": 79.5982, "matched_fragments": 187, "total_fragments": 511, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.86", "min_intra_species_ani": "99.72", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_019117445.1", "gtdb_species": "s__Limosilactobacillus excrementigallinarum", "ani": 77.9812, "matched_fragments": 81, "total_fragments": 511, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.52", "min_intra_species_ani": "96.52", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "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__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Limosilactobacillus", "s__Limosilactobacillus vaginalis" ], "_genome_taxon": [ "Limosilactobacillus", "vaginalis", "d__Bacteria", "p__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Limosilactobacillus", "s__Limosilactobacillus vaginalis", "Bacteria", "Bacillota", "Bacilli", "Lactobacillales", "Lactobacillaceae", "Limosilactobacillus", "Limosilactobacillus", "vaginalis" ], "_meo": [ { "id": "MEO_0000523", "label": "vagina" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }