{ "type": "genome", "identifier": "GCF_004403345.1", "organism": "Cryobacterium lyxosi", "title": "Cryobacterium lyxosi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Microbiology, Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004403345.1", "bioproject": "PRJNA224116", "biosample": "SAMN11157775", "wgs_master": "SOGT00000000.1", "refseq_category": "reference genome", "taxid": "1259228", "species_taxid": "1259228", "organism_name": "Cryobacterium lyxosi", "infraspecific_name": "strain=TMT1-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/26", "asm_name": "ASM440334v1", "asm_submitter": "Institute of Microbiology, Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_004403345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/403/345/GCF_004403345.1_ASM440334v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3539219", "genome_size_ungapped": "3539219", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004403345.1-RS_2024_04_01", "annotation_date": "2024-04-01", "total_gene_count": "3296", "protein_coding_gene_count": "3191", "non_coding_gene_count": "52", "pubmed_id": "32090405" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-26", "dateModified": "2019-03-26", "datePublished": "2019-03-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Cryobacterium lyxosi" ], "sample_taxid": [ "1259228" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "0.992 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)": "3539219", "Number of Sequences": "20", "Longest Sequences (bp)": "508022", "N50 (bp)": "293819", "Gap Ratio (%)": "0.000283", "GCcontent (%)": "63.5", "Number of CDSs": "3307", "Average Protein Length": "316.6", "Coding Ratio (%)": "88.8", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cryobacterium aureum", "strain": "strain=Hh31", "accession": "GCA_002954245.1", "taxid": 995037, "species_taxid": 995037, "relation_to_type": "type", "validated": true, "ani": 86.1163, "matched_fragments": 828, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium flavum", "strain": "strain=Hh8", "accession": "GCA_004402625.1", "taxid": 1424659, "species_taxid": 1424659, "relation_to_type": "type", "validated": true, "ani": 85.9469, "matched_fragments": 825, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium flavum", "strain": "strain=CGMCC 1.11215", "accession": "GCA_900103805.1", "taxid": 1424659, "species_taxid": 1424659, "relation_to_type": "type", "validated": true, "ani": 85.9314, "matched_fragments": 828, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium ruanii", "strain": "strain=Sr36", "accession": "GCA_004404055.1", "taxid": 1259197, "species_taxid": 1259197, "relation_to_type": "type", "validated": true, "ani": 85.5459, "matched_fragments": 807, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium luteum", "strain": "strain=Hh15", "accession": "GCA_004402515.1", "taxid": 1424661, "species_taxid": 1424661, "relation_to_type": "type", "validated": true, "ani": 84.9847, "matched_fragments": 800, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium luteum", "strain": "strain=CGMCC 1.11210", "accession": "GCA_900110125.1", "taxid": 1424661, "species_taxid": 1424661, "relation_to_type": "type", "validated": true, "ani": 84.9342, "matched_fragments": 811, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium levicorallinum", "strain": "strain=NBRC 107883", "accession": "GCA_007992355.1", "taxid": 995038, "species_taxid": 995038, "relation_to_type": "type", "validated": true, "ani": 84.6613, "matched_fragments": 793, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium levicorallinum", "strain": "strain=GMCC 1.11211", "accession": "GCA_900113585.1", "taxid": 995038, "species_taxid": 995038, "relation_to_type": "type", "validated": true, "ani": 84.6425, "matched_fragments": 796, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium levicorallinum", "strain": "strain=Hh34", "accession": "GCA_004402405.1", "taxid": 995038, "species_taxid": 995038, "relation_to_type": "type", "validated": true, "ani": 84.5638, "matched_fragments": 803, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium arcticum", "strain": "strain=SK-1", "accession": "GCA_003185895.1", "taxid": 670052, "species_taxid": 670052, "relation_to_type": "type", "validated": true, "ani": 79.7038, "matched_fragments": 451, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces cavernae", "strain": "strain=SYSU K20354", "accession": "GCA_021044935.1", "taxid": 2898659, "species_taxid": 2898659, "relation_to_type": "type", "validated": true, "ani": 77.9626, "matched_fragments": 266, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces archimandritae", "strain": "strain=G127AT", "accession": "GCA_018024495.1", "taxid": 2781962, "species_taxid": 2781962, "relation_to_type": "type", "validated": true, "ani": 77.5684, "matched_fragments": 251, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. insidiosus", "strain": "strain=ATCC 10253", "accession": "GCA_003076355.1", "taxid": 33014, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 77.3544, "matched_fragments": 225, "total_fragments": 1168, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002929825.1", "gtdb_species": "s__Cryobacterium sp002929825", "ani": 95.0227, "matched_fragments": 959, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.15", "min_intra_species_ani": "95.07", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_002929505.1", "gtdb_species": "s__Cryobacterium sp002929505", "ani": 94.3191, "matched_fragments": 977, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "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_004403185.1", "gtdb_species": "s__Cryobacterium sp004403185", "ani": 89.8294, "matched_fragments": 853, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "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_002929495.1", "gtdb_species": "s__Cryobacterium sp002929495", "ani": 89.546, "matched_fragments": 864, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.09", "min_intra_species_ani": "97.09", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004403985.1", "gtdb_species": "s__Cryobacterium sp004403985", "ani": 86.7039, "matched_fragments": 841, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002954245.1", "gtdb_species": "s__Cryobacterium aureum", "ani": 86.0962, "matched_fragments": 829, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "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_900103805.1", "gtdb_species": "s__Cryobacterium flavum", "ani": 85.9147, "matched_fragments": 830, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "97.38", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_004402535.1", "gtdb_species": "s__Cryobacterium sp004402535", "ani": 85.6302, "matched_fragments": 767, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "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_004404055.1", "gtdb_species": "s__Cryobacterium ruanii", "ani": 85.5567, "matched_fragments": 806, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "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_004402405.1", "gtdb_species": "s__Cryobacterium levicorallinum", "ani": 84.5638, "matched_fragments": 803, "total_fragments": 1168, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.20", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.78", "num_clustered_genomes": 9, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.309, "cell_length": 0.078, "doubling_h": null, "growth_tmp": 15.5, "optimum_tmp": 19.125, "optimum_ph": 7.25, "genome_size": 3930741.888, "gc_content": 66.834, "coding_genes": 3934.0, "rRNA16S_genes": 3.0, "tRNA_genes": 51.0, "gram_stain": 1.0, "sporulation": null, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Cryobacterium", "lyxosi" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }