{ "type": "genome", "identifier": "GCF_000738005.1", "organism": "Bifidobacterium crudilactis", "title": "Bifidobacterium crudilactis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Liege", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000738005.1", "bioproject": "PRJNA224116", "biosample": "SAMN02699097", "wgs_master": "JHAL00000000.1", "refseq_category": "reference genome", "taxid": "327277", "species_taxid": "327277", "organism_name": "Bifidobacterium crudilactis", "infraspecific_name": "strain=LMG 23609", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/08/06", "asm_name": "ASM73800v1", "asm_submitter": "University of Liege", "gbrs_paired_asm": "GCA_000738005.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/738/005/GCF_000738005.1_ASM73800v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2362816", "genome_size_ungapped": "2362816", "gc_percent": "57.500000", "replicon_count": "0", "scaffold_count": "6", "contig_count": "6", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000738005.1-RS_2024_06_16", "annotation_date": "2024-06-16", "total_gene_count": "1934", "protein_coding_gene_count": "1854", "non_coding_gene_count": "54", "pubmed_id": "25107967" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-08-06", "dateModified": "2014-08-06", "datePublished": "2014-08-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium crudilactis" ], "sample_taxid": [ "327277" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France" ], "sample_host_location_id": [], "data_size": "0.669 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)": "2362816", "Number of Sequences": "6", "Longest Sequences (bp)": "1716957", "N50 (bp)": "1716957", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "57.7", "Number of CDSs": "1937", "Average Protein Length": "349.1", "Coding Ratio (%)": "85.9", "Number of rRNAs": "2", "Number of tRNAs": "46", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium crudilactis", "strain": "strain=LMG 23609", "accession": "GCA_000738005.1", "taxid": 327277, "species_taxid": 327277, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 785, "total_fragments": 785, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium psychraerophilum", "strain": "strain=DSM 22366", "accession": "GCA_002813205.1", "taxid": 218140, "species_taxid": 218140, "relation_to_type": "type", "validated": true, "ani": 80.9617, "matched_fragments": 399, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium psychraerophilum", "strain": "strain=DSM 22366", "accession": "GCA_000771565.1", "taxid": 218140, "species_taxid": 218140, "relation_to_type": "type", "validated": true, "ani": 80.9005, "matched_fragments": 380, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium psychraerophilum", "strain": "strain=LMG 21775", "accession": "GCA_000741705.1", "taxid": 218140, "species_taxid": 218140, "relation_to_type": "type", "validated": true, "ani": 80.8555, "matched_fragments": 385, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium aquikefiri", "strain": "strain=LMG 28769", "accession": "GCA_002259795.1", "taxid": 1653207, "species_taxid": 1653207, "relation_to_type": "type", "validated": true, "ani": 78.5471, "matched_fragments": 120, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium lemurum", "strain": "strain=DSM 28807", "accession": "GCA_002259665.1", "taxid": 1603886, "species_taxid": 1603886, "relation_to_type": "type", "validated": true, "ani": 78.1085, "matched_fragments": 129, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium eulemuris", "strain": "strain=DSM 100216", "accession": "GCA_014898155.1", "taxid": 1765219, "species_taxid": 1765219, "relation_to_type": "type", "validated": true, "ani": 78.0174, "matched_fragments": 140, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium 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"accession": "GCA_000770985.1", "taxid": 158787, "species_taxid": 158787, "relation_to_type": "type", "validated": true, "ani": 77.8338, "matched_fragments": 142, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium eulemuris", "strain": "strain=DSM 100216", "accession": "GCA_002259685.1", "taxid": 1765219, "species_taxid": 1765219, "relation_to_type": "type", "validated": true, "ani": 77.8124, "matched_fragments": 137, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium saguinibicoloris", "strain": "strain=79T10", "accession": "GCA_019331725.1", "taxid": 2834433, "species_taxid": 2834433, "relation_to_type": "type", "validated": true, "ani": 77.7431, "matched_fragments": 130, "total_fragments": 785, "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": 77.678, "matched_fragments": 100, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium biavatii", "strain": "strain=DSM 23969", "accession": "GCA_000741165.1", "taxid": 762212, "species_taxid": 762212, "relation_to_type": "type", "validated": true, "ani": 77.6258, "matched_fragments": 116, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium actinocoloniiforme", "strain": "strain=DSM 22766", "accession": "GCA_000771585.1", "taxid": 638619, "species_taxid": 638619, "relation_to_type": "type", "validated": true, "ani": 77.5432, "matched_fragments": 91, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium biavatii", "strain": "strain=DSM 23969", "accession": "GCA_000771645.1", "taxid": 762212, "species_taxid": 762212, "relation_to_type": "type", "validated": true, "ani": 77.4925, "matched_fragments": 120, "total_fragments": 785, "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": 77.2684, "matched_fragments": 113, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000738005.1", "gtdb_species": "s__Bifidobacterium crudilactis", "ani": 100.0, "matched_fragments": 785, "total_fragments": 785, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.51", "min_intra_species_ani": "97.51", 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"98.93", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002259795.1", "gtdb_species": "s__Bifidobacterium aquikefiri", "ani": 78.5437, "matched_fragments": 119, "total_fragments": 785, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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_014898175.1", "gtdb_species": "s__Bifidobacterium lemurum", "ani": 78.1692, "matched_fragments": 133, "total_fragments": 785, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", 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"mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002802905.1", "gtdb_species": "s__Galliscardovia simiarum", "ani": 77.8711, "matched_fragments": 147, "total_fragments": 785, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.16", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002802875.1", "gtdb_species": "s__Galliscardovia primatium", "ani": 77.848, "matched_fragments": 147, "total_fragments": 785, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000771405.1", "gtdb_species": "s__Bifidobacterium pullorum", "ani": 77.7418, "matched_fragments": 146, "total_fragments": 785, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "97.42", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000770925.1", "gtdb_species": "s__Bifidobacterium ruminantium", "ani": 77.7169, "matched_fragments": 139, "total_fragments": 785, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "97.77", "mean_intra_species_af": "0.92", 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