{ "type": "genome", "identifier": "GCF_004365915.1", "organism": "Cryobacterium psychrophilum", "title": "Cryobacterium psychrophilum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004365915.1", "bioproject": "PRJNA224116", "biosample": "SAMN10363323", "wgs_master": "SODI00000000.1", "refseq_category": "reference genome", "taxid": "41988", "species_taxid": "41988", "organism_name": "Cryobacterium psychrophilum", "infraspecific_name": "strain=DSM 4854", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436591v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004365915.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/365/915/GCF_004365915.1_ASM436591v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3677616", "genome_size_ungapped": "3677616", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004365915.1-RS_2024_04_19", "annotation_date": "2024-04-19", "total_gene_count": "3499", "protein_coding_gene_count": "3354", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Cryobacterium psychrophilum" ], "sample_taxid": [ "41988" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Antarctica" ], "sample_host_location_id": [], "data_size": "1.024 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)": "3677616", "Number of Sequences": "2", "Longest Sequences (bp)": "3565758", "N50 (bp)": "3565758", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.8", "Number of CDSs": "3509", "Average Protein Length": "310.7", "Coding Ratio (%)": "88.9", "Number of rRNAs": "13", "Number of tRNAs": "51", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cryobacterium psychrophilum", "strain": "strain=DSM 4854", "accession": "GCA_004365915.1", "taxid": 41988, "species_taxid": 41988, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1223, "total_fragments": 1225, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cryobacterium roopkundense", "strain": "strain=DSM 21065", "accession": "GCA_014200405.1", "taxid": 1001240, "species_taxid": 1001240, "relation_to_type": "type", "validated": true, "ani": 81.6084, "matched_fragments": 656, "total_fragments": 1225, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium roopkundense", "strain": "strain=RuG17", "accession": "GCA_000764165.1", "taxid": 1001240, "species_taxid": 1001240, "relation_to_type": "type", "validated": true, "ani": 81.5874, "matched_fragments": 631, "total_fragments": 1225, "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": 80.3985, "matched_fragments": 541, "total_fragments": 1225, "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": 80.3297, "matched_fragments": 544, "total_fragments": 1225, "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": 80.3137, "matched_fragments": 509, "total_fragments": 1225, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium melibiosiphilum", "strain": "strain=Hh39", "accession": "GCA_003602235.1", "taxid": 995039, "species_taxid": 995039, "relation_to_type": "type", "validated": true, "ani": 80.2206, "matched_fragments": 573, "total_fragments": 1225, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium aureum", "strain": "strain=Hh31", "accession": "GCA_002954245.1", "taxid": 995037, "species_taxid": 995037, "relation_to_type": "type", "validated": true, "ani": 80.1628, "matched_fragments": 518, "total_fragments": 1225, "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": 80.1067, "matched_fragments": 510, "total_fragments": 1225, "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": 80.0857, "matched_fragments": 520, "total_fragments": 1225, "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": 80.0848, "matched_fragments": 513, "total_fragments": 1225, "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": 79.9342, "matched_fragments": 498, "total_fragments": 1225, "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": 79.8219, "matched_fragments": 456, "total_fragments": 1225, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium soli", "strain": "strain=GCJ02", "accession": "GCA_003611035.1", "taxid": 2220095, "species_taxid": 2220095, "relation_to_type": "type", "validated": true, "ani": 79.8081, "matched_fragments": 474, "total_fragments": 1225, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. tessellarius", "strain": "strain=ATCC 33566", "accession": "GCA_002240635.1", "taxid": 31965, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 77.9199, "matched_fragments": 258, "total_fragments": 1225, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces mariniharenae", "strain": "strain=NEAU-184", "accession": "GCA_008122505.1", "taxid": 2604423, "species_taxid": 2604423, "relation_to_type": "type", "validated": true, "ani": 77.8871, "matched_fragments": 302, "total_fragments": 1225, "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": 77.5715, "matched_fragments": 289, "total_fragments": 1225, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces humatus", "strain": "strain=JCM 14319", "accession": "GCA_021228295.1", "taxid": 279573, "species_taxid": 279573, "relation_to_type": "type", "validated": true, "ani": 77.4723, "matched_fragments": 298, "total_fragments": 1225, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004365915.1", "gtdb_species": "s__Cryobacterium psychrophilum", "ani": 100.0, "matched_fragments": 1224, "total_fragments": 1225, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_014200405.1", "gtdb_species": "s__Cryobacterium roopkundense", "ani": 81.5864, "matched_fragments": 656, "total_fragments": 1225, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000738085.1", "gtdb_species": "s__Cryobacterium sp000738085", "ani": 80.858, "matched_fragments": 590, "total_fragments": 1225, "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_015751745.1", "gtdb_species": "s__Cryobacterium sp015751745", "ani": 80.6951, "matched_fragments": 542, "total_fragments": 1225, "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_004402535.1", "gtdb_species": "s__Cryobacterium sp004402535", "ani": 80.4536, "matched_fragments": 532, "total_fragments": 1225, "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": 80.3927, "matched_fragments": 542, "total_fragments": 1225, "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_003602235.1", "gtdb_species": "s__Cryobacterium sp003602235", "ani": 80.2392, "matched_fragments": 572, "total_fragments": 1225, "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": 80.0753, "matched_fragments": 521, "total_fragments": 1225, "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": "-" }, { "accession": "GCF_004403305.1", "gtdb_species": "s__Cryobacterium sp004403305", "ani": 80.0718, "matched_fragments": 544, "total_fragments": 1225, "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_015752155.1", "gtdb_species": "s__Cryobacterium sp015752155", "ani": 80.0159, "matched_fragments": 527, "total_fragments": 1225, "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_004403985.1", "gtdb_species": "s__Cryobacterium sp004403985", "ani": 79.9582, "matched_fragments": 457, "total_fragments": 1225, "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_004403185.1", "gtdb_species": "s__Cryobacterium sp004403185", "ani": 79.9512, "matched_fragments": 466, "total_fragments": 1225, "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_002929825.1", "gtdb_species": "s__Cryobacterium sp002929825", "ani": 79.7923, "matched_fragments": 466, "total_fragments": 1225, "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": "-" }, { "accession": "GCF_002929555.1", "gtdb_species": "s__Cryobacterium sp002929555", "ani": 79.5812, "matched_fragments": 472, "total_fragments": 1225, "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_004403945.1", "gtdb_species": "s__Cryobacterium sp004403945", "ani": 79.507, "matched_fragments": 464, "total_fragments": 1225, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 10.0, "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", "psychrophilum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }