{ "type": "genome", "identifier": "GCF_003627095.1", "organism": "Lactococcus allomyrinae", "title": "Lactococcus allomyrinae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003627095.1", "bioproject": "PRJNA224116", "biosample": "SAMN10141031", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2419773", "species_taxid": "2419773", "organism_name": "Lactococcus allomyrinae", "infraspecific_name": "strain=1JSPR-7", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/07", "asm_name": "ASM362709v1", "asm_submitter": "National Institute of Agricultural Sciences", "gbrs_paired_asm": "GCA_003627095.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/627/095/GCF_003627095.1_ASM362709v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2758410", "genome_size_ungapped": "2758410", "gc_percent": "37.500000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003627095.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2678", "protein_coding_gene_count": "2521", "non_coding_gene_count": "89", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-07", "dateModified": "2018-10-07", "datePublished": "2018-10-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Lactococcus allomyrinae" ], "sample_taxid": [ "2419773" ], "sample_host_organism": [ "Trypoxylus dichotomus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Jeonju" ], "sample_host_location_id": [], "data_size": "0.772 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)": "2758410", "Number of Sequences": "3", "Longest Sequences (bp)": "2695154", "N50 (bp)": "2695154", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "37.4", "Number of CDSs": "2647", "Average Protein Length": "290.0", "Coding Ratio (%)": "83.5", "Number of rRNAs": "19", "Number of tRNAs": "66", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lactococcus allomyrinae", "strain": "strain=1JSPR-7", "accession": "GCA_003627095.1", "taxid": 2419773, "species_taxid": 2419773, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 916, "total_fragments": 918, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactococcus protaetiae", "strain": "strain=KACC 19320", "accession": "GCA_006965445.1", "taxid": 2592653, "species_taxid": 2592653, "relation_to_type": "type", "validated": true, "ani": 93.6507, "matched_fragments": 767, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "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": 79.853, "matched_fragments": 304, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactococcus lactis", "strain": "strain=ATCC 19435", "accession": "GCA_900099625.1", "taxid": 1358, "species_taxid": 1358, "relation_to_type": "type", 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"total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactococcus fujiensis", "strain": "strain=JCM 16395", "accession": "GCA_002441655.1", "taxid": 610251, "species_taxid": 610251, "relation_to_type": "type", "validated": true, "ani": 77.5356, "matched_fragments": 121, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003627095.1", "gtdb_species": "s__Lactococcus allomyrinae", "ani": 100.0, "matched_fragments": 917, "total_fragments": 918, "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": "conclusive" }, { "accession": "GCF_006965445.1", "gtdb_species": "s__Lactococcus sp006965445", "ani": 93.6502, "matched_fragments": 768, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.72", "min_intra_species_ani": "98.72", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004210295.1", "gtdb_species": "s__Lactococcus sp004210295", "ani": 79.7722, "matched_fragments": 259, "total_fragments": 918, "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_900099625.1", "gtdb_species": "s__Lactococcus lactis", 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Lactococcus", "allomyrinae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }