{ "type": "genome", "identifier": "GCF_019331675.1", "organism": "Bifidobacterium miconisargentati", "title": "Bifidobacterium miconisargentati", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Parma", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019331675.1", "bioproject": "PRJNA224116", "biosample": "SAMN19031632", "wgs_master": "JAHBBJ000000000.1", "refseq_category": "reference genome", "taxid": "2834437", "species_taxid": "2834437", "organism_name": "Bifidobacterium miconisargentati", "infraspecific_name": "strain=82T25", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/23", "asm_name": "ASM1933167v1", "asm_submitter": "University of Parma", "gbrs_paired_asm": "GCA_019331675.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/331/675/GCF_019331675.1_ASM1933167v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2983671", "genome_size_ungapped": "2983671", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "39", "contig_count": "39", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019331675.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2386", "protein_coding_gene_count": "2278", "non_coding_gene_count": "69", "pubmed_id": "34715437" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-07-23", "dateModified": "2021-07-23", "datePublished": "2021-07-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium miconisargentati" ], "sample_taxid": [ "2834437" ], "sample_host_organism": [ "Mico argentatus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain" ], "sample_host_location_id": [], "data_size": "0.830 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)": "2983671", "Number of Sequences": "39", "Longest Sequences (bp)": "312657", "N50 (bp)": "147744", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.2", "Number of CDSs": "2324", "Average Protein Length": "364.7", "Coding Ratio (%)": "85.2", "Number of rRNAs": "1", "Number of tRNAs": "60", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium miconisargentati", "strain": "strain=82T25", "accession": "GCA_019331675.1", "taxid": 2834437, "species_taxid": 2834437, "relation_to_type": "type", "validated": true, "ani": 100.0, 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium longum subsp. suillum", "strain": "strain=JCM 19995", "accession": "GCA_017132755.1", "taxid": 1931217, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 84.2123, "matched_fragments": 511, "total_fragments": 974, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium longum subsp. infantis", "strain": "strain=DSM 20088", "accession": "GCA_000771105.1", "taxid": 1682, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 84.159, "matched_fragments": 476, "total_fragments": 974, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium longum subsp. infantis", "strain": "strain=NCTC11817", "accession": "GCA_900637215.1", "taxid": 1682, "species_taxid": 216816, "relation_to_type": "type", "validated": true, "ani": 84.1438, "matched_fragments": 491, "total_fragments": 974, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium amazonense", "strain": "strain=MA1", "accession": "GCA_018555435.2", "taxid": 2809027, "species_taxid": 2809027, "relation_to_type": "type", "validated": true, "ani": 83.2762, "matched_fragments": 521, "total_fragments": 974, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium pseudolongum subsp. pseudolongum", "strain": "strain=ATCC 25526", "accession": "GCA_022691205.1", "taxid": 31954, "species_taxid": 1694, "relation_to_type": "type", "validated": true, "ani": 79.5121, "matched_fragments": 293, "total_fragments": 974, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium mizhiense", "strain": "strain=S053-2", "accession": "GCA_020884755.1", "taxid": 2879940, "species_taxid": 2879940, "relation_to_type": "type", "validated": true, "ani": 78.3324, "matched_fragments": 198, "total_fragments": 974, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas avistercoris", "strain": "strain=Sa3CUA2", "accession": "GCA_014836445.1", "taxid": 2762242, "species_taxid": 2762242, "relation_to_type": "type", "validated": true, "ani": 76.0072, "matched_fragments": 104, "total_fragments": 974, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018555355.1", "gtdb_species": "s__Bifidobacterium sp018555355", "ani": 96.2048, "matched_fragments": 815, "total_fragments": 974, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.26", "min_intra_species_ani": "96.26", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003129905.1", "gtdb_species": 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"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 }, "_genome_taxon": [ "Bifidobacterium", "miconisargentati" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }