{ "type": "genome", "identifier": "GCF_003293675.1", "organism": "Gardnerella leopoldii", "title": "Gardnerella leopoldii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ghent University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003293675.1", "bioproject": "PRJNA224116", "biosample": "SAMN09373173", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2792978", "species_taxid": "2792978", "organism_name": "Gardnerella leopoldii", "infraspecific_name": "strain=UGent 06.41", "isolate": "na", "version_status": "latest", "assembly_level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/09", "asm_name": "ASM329367v1", "asm_submitter": "Ghent University", "gbrs_paired_asm": "GCA_003293675.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/293/675/GCF_003293675.1_ASM329367v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1563545", "genome_size_ungapped": "1563445", "gc_percent": "42.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003293675.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "1249", "protein_coding_gene_count": "1179", "non_coding_gene_count": "54", "pubmed_id": "30648938" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-09", "dateModified": "2018-07-09", "datePublished": "2018-07-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Gardnerella leopoldii" ], "sample_taxid": [ "2792978" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "commensal/bacterial vaginosis" ], "sample_host_disease_id": [], "sample_host_location": [ "Belgium: Ghent" ], "sample_host_location_id": [], "data_size": "0.441 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)": "1563445", "Number of Sequences": "1", "Longest Sequences (bp)": "1563445", "N50 (bp)": "1563445", "Gap Ratio (%)": "0.000512", "GCcontent (%)": "42.1", "Number of CDSs": "1197", "Average Protein Length": "378.2", "Coding Ratio (%)": "86.9", "Number of rRNAs": "6", "Number of tRNAs": "45", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gardnerella leopoldii", "strain": "strain=UGent 06.41", "accession": "GCA_003293675.1", "taxid": 2792978, "species_taxid": 2792978, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 521, "total_fragments": 521, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Gardnerella swidsinskii", "strain": "strain=GS 9838-1", "accession": "GCA_003397705.1", "taxid": 2792979, "species_taxid": 2792979, "relation_to_type": "type", "validated": true, "ani": 95.6629, "matched_fragments": 458, "total_fragments": 521, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Gardnerella vaginalis", "strain": "strain=JCM 11026", "accession": "GCA_001042655.1", "taxid": 2702, "species_taxid": 2702, "relation_to_type": "suspected-type", "validated": true, "ani": 83.8714, "matched_fragments": 282, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gardnerella vaginalis", "strain": "strain=DSM 4944", "accession": "GCA_900105405.1", "taxid": 2702, "species_taxid": 2702, "relation_to_type": "suspected-type", "validated": true, "ani": 83.7526, "matched_fragments": 279, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gardnerella vaginalis", "strain": "strain=ATCC 14018", "accession": "GCA_003397685.1", "taxid": 2702, "species_taxid": 2702, "relation_to_type": "suspected-type", "validated": true, "ani": 83.6655, "matched_fragments": 284, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gardnerella vaginalis", "strain": "strain=ATCC 14018", "accession": "GCA_000178355.1", "taxid": 2702, "species_taxid": 2702, "relation_to_type": "suspected-type", "validated": true, "ani": 83.2787, "matched_fragments": 246, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gardnerella piotii", "strain": "strain=UGent 18.01", "accession": "GCA_003397585.1", "taxid": 2792977, "species_taxid": 2792977, "relation_to_type": "type", "validated": true, "ani": 82.7427, "matched_fragments": 277, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Galliscardovia ingluviei", "strain": "strain=CCM 8606", "accession": "GCA_014635685.1", "taxid": 1769422, "species_taxid": 1769422, "relation_to_type": "type", "validated": true, "ani": 77.7414, "matched_fragments": 50, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alloscardovia omnicolens", "strain": "strain=DSM 21503", "accession": "GCA_000420505.1", "taxid": 419015, "species_taxid": 419015, "relation_to_type": "type", "validated": true, "ani": 77.4851, "matched_fragments": 53, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003293675.1", "gtdb_species": "s__Bifidobacterium leopoldii", "ani": 100.0, "matched_fragments": 521, "total_fragments": 521, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.706, "mean_intra_species_ani": "98.89", "min_intra_species_ani": "98.40", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 16, "status": "conclusive" }, { "accession": "GCA_003585845.1", "gtdb_species": "s__Bifidobacterium sp003585845", "ani": 95.706, "matched_fragments": 472, "total_fragments": 521, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.706, "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": "conclusive" }, { "accession": "GCF_003397705.1", "gtdb_species": "s__Bifidobacterium swidsinskii", "ani": 95.6629, "matched_fragments": 458, "total_fragments": 521, 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