{ "type": "genome", "identifier": "GCF_004354485.1", "organism": "Lactococcus lactis subsp. lactis", "title": "Lactococcus lactis subsp. lactis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Carlsberg Research Laboratory", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004354485.1", "bioproject": "PRJNA224116", "biosample": "SAMN08554999", "wgs_master": "PUFC00000000.1", "refseq_category": "na", "taxid": "1360", "species_taxid": "1358", "organism_name": "Lactococcus lactis subsp. lactis", "infraspecific_name": "strain=ATCC 19435", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/18", "asm_name": "ASM435448v1", "asm_submitter": "Carlsberg Research Laboratory", "gbrs_paired_asm": "GCA_004354485.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/354/485/GCF_004354485.1_ASM435448v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2627820", "genome_size_ungapped": "2627520", "gc_percent": "35.500000", "replicon_count": "0", "scaffold_count": "82", "contig_count": "82", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004354485.1-RS_2024_04_08", "annotation_date": "2024-04-08", "total_gene_count": "2723", "protein_coding_gene_count": "2538", "non_coding_gene_count": "95", "pubmed_id": "30830251" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-18", "dateModified": "2019-03-18", "datePublished": "2019-03-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Lactococcus lactis subsp. lactis" ], "sample_taxid": [ "1360" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Denmark" ], "sample_host_location_id": [], "data_size": "0.734 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)": "2627820", "Number of Sequences": "82", "Longest Sequences (bp)": "444394", "N50 (bp)": "161786", "Gap Ratio (%)": "0.011454", "GCcontent (%)": "35.4", "Number of CDSs": "2593", "Average Protein Length": "284.3", "Coding Ratio (%)": "84.2", "Number of rRNAs": "25", "Number of tRNAs": "64", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lactococcus lactis subsp. lactis", "strain": "strain=ATCC 19435", "accession": "GCA_004354485.1", "taxid": 1360, "species_taxid": 1358, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 837, "total_fragments": 842, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactococcus lactis", "strain": "strain=FDAARGOS_865", "accession": "GCA_016028835.1", "taxid": 1358, "species_taxid": 1358, "relation_to_type": "type", "validated": true, "ani": 99.9884, "matched_fragments": 827, "total_fragments": 842, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactococcus lactis subsp. lactis", "strain": "strain=NBRC 100933", "accession": "GCA_001514475.1", "taxid": 1360, "species_taxid": 1358, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9763, "matched_fragments": 813, "total_fragments": 842, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactococcus lactis subsp. lactis", "strain": "strain=ATCC 19435", "accession": "GCA_001456385.1", "taxid": 1360, "species_taxid": 1358, "relation_to_type": "type", "validated": true, "ani": 99.9526, "matched_fragments": 784, "total_fragments": 842, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactococcus lactis", "strain": "strain=ATCC 19435", "accession": "GCA_900099625.1", "taxid": 1358, "species_taxid": 1358, "relation_to_type": "type", "validated": true, "ani": 99.9405, "matched_fragments": 804, "total_fragments": 842, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactococcus lactis subsp. hordniae", "strain": "strain=DSM 20450", "accession": "GCA_002441785.1", "taxid": 203404, "species_taxid": 1358, "relation_to_type": "type", "validated": true, "ani": 97.2, "matched_fragments": 636, "total_fragments": 842, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactococcus lactis subsp. hordniae", "strain": "strain=CCUG 32210T", "accession": "GCA_008692945.1", "taxid": 203404, "species_taxid": 1358, "relation_to_type": "type", "validated": true, "ani": 97.1368, "matched_fragments": 645, "total_fragments": 842, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactococcus 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"strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900099625.1", "gtdb_species": "s__Lactococcus lactis", "ani": 99.9405, "matched_fragments": 804, "total_fragments": 842, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.37", "min_intra_species_ani": "97.03", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.82", "num_clustered_genomes": 223, "status": "conclusive" }, { "accession": "GCF_001591705.1", "gtdb_species": "s__Lactococcus cremoris", "ani": 87.9356, "matched_fragments": 578, "total_fragments": 842, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "97.45", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.82", "num_clustered_genomes": 70, "status": "-" }, { 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hircilactis", "ani": 79.9493, "matched_fragments": 195, "total_fragments": 842, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus", "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_018403765.1", "gtdb_species": "s__Lactococcus nasutitermitis", "ani": 79.5629, "matched_fragments": 190, "total_fragments": 842, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus", "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_003627095.1", "gtdb_species": "s__Lactococcus allomyrinae", "ani": 79.4695, "matched_fragments": 310, 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