{ "type": "genome", "identifier": "GCF_002441715.1", "organism": "Lactococcus plantarum", "title": "Lactococcus plantarum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Inner Mongolia Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002441715.1", "bioproject": "PRJNA224116", "biosample": "SAMN03267153", "wgs_master": "JXJX00000000.1", "refseq_category": "na", "taxid": "1365", "species_taxid": "1365", "organism_name": "Lactococcus plantarum", "infraspecific_name": "strain=DSM 20686", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/10/04", "asm_name": "ASM244171v1", "asm_submitter": "Inner Mongolia Agricultural University", "gbrs_paired_asm": "GCA_002441715.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/441/715/GCF_002441715.1_ASM244171v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1989201", "genome_size_ungapped": "1989201", "gc_percent": "37.000000", "replicon_count": "0", "scaffold_count": "43", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002441715.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "1905", "protein_coding_gene_count": "1841", "non_coding_gene_count": "37", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-10-04", "dateModified": "2017-10-04", "datePublished": "2017-10-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Lactococcus plantarum" ], "sample_taxid": [ "1365" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.562 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)": "1989201", "Number of Sequences": "43", "Longest Sequences (bp)": "214459", "N50 (bp)": "162283", "Gap Ratio (%)": "0.000503", "GCcontent (%)": "36.8", "Number of CDSs": "1857", "Average Protein Length": "310.6", "Coding Ratio (%)": "87.0", "Number of rRNAs": "3", "Number of tRNAs": "30", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lactococcus plantarum", "strain": "strain=DSM 20686", "accession": "GCA_002441715.1", "taxid": 1365, "species_taxid": 1365, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 642, "total_fragments": 644, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactococcus paracarnosus", "strain": "strain=TMW 2.1615", "accession": "GCA_006770285.1", "taxid": 2749962, "species_taxid": 2749962, "relation_to_type": "type", "validated": true, "ani": 80.3053, "matched_fragments": 309, "total_fragments": 644, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactococcus piscium", "strain": "strain=DSM 6634", "accession": "GCA_002441695.1", "taxid": 1364, "species_taxid": 1364, "relation_to_type": "suspected-type", "validated": true, "ani": 80.0108, "matched_fragments": 310, "total_fragments": 644, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactococcus carnosus", "strain": "strain=TMW 2.1612", "accession": "GCA_006770265.1", "taxid": 2749961, "species_taxid": 2749961, "relation_to_type": "type", "validated": true, "ani": 79.973, "matched_fragments": 315, "total_fragments": 644, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactococcus 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"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_006770265.1", "gtdb_species": "s__Lactococcus_A carnosus", "ani": 79.973, "matched_fragments": 315, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.28", "min_intra_species_ani": "95.96", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_002441885.1", "gtdb_species": "s__Lactococcus_A chungangensis", "ani": 79.7118, "matched_fragments": 224, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_013449735.1", "gtdb_species": "s__Lactococcus_A laudensis", "ani": 79.5504, "matched_fragments": 220, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001591765.1", "gtdb_species": "s__Lactococcus_A raffinolactis", "ani": 79.3046, "matched_fragments": 202, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_002260845.1", "gtdb_species": "s__Lactococcus_A reticulitermitis", "ani": 78.6314, "matched_fragments": 175, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": -0.302, "doubling_h": -0.114, "growth_tmp": 30.0, "optimum_tmp": 30.902, "optimum_ph": 5.9, "genome_size": 1974929.0, "gc_content": 36.73, "coding_genes": 2184.408, "rRNA16S_genes": 4.75, "tRNA_genes": 58.609, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.857, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.142, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Lactococcus", "plantarum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }