{ "type": "genome", "identifier": "GCF_900156665.1", "organism": "Corynebacterium appendicis CIP 107643", "title": "Corynebacterium appendicis CIP 107643", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900156665.1", "bioproject": "PRJNA224116", "biosample": "SAMN05444817", "wgs_master": "FTOF00000000.1", "refseq_category": "na", "taxid": "1161099", "species_taxid": "163202", "organism_name": "Corynebacterium appendicis CIP 107643", "infraspecific_name": "strain=DSM 44531", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/01/14", "asm_name": "IMG-taxon 2681813517 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900156665.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/156/665/GCF_900156665.1_IMG-taxon_2681813517_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2248056", "genome_size_ungapped": "2248056", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "32", "contig_count": "32", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-26", "total_gene_count": "2213", "protein_coding_gene_count": "2093", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-01-14", "dateModified": "2017-01-14", "datePublished": "2017-01-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Corynebacterium appendicis CIP 107643" ], "sample_taxid": [ "1161099" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.628 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.54, "contamination": 0.52, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2248056", "Number of Sequences": "32", "Longest Sequences (bp)": "366149", "N50 (bp)": "194818", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.3", "Number of CDSs": "2154", "Average Protein Length": "313.3", "Coding Ratio (%)": "90.1", "Number of rRNAs": "3", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Corynebacterium appendicis", "strain": "strain=DSM 44531", "accession": "GCA_900156665.1", "taxid": 163202, "species_taxid": 163202, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 729, "total_fragments": 729, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Corynebacterium urinipleomorphum", "strain": "strain=Marseille-P2799", "accession": "GCA_900155535.1", "taxid": 1852380, "species_taxid": 1852380, "relation_to_type": "type", "validated": true, "ani": 85.1443, "matched_fragments": 581, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium mycetoides", "strain": "strain=DSM 20632", "accession": "GCA_900103625.1", "taxid": 38302, "species_taxid": 38302, "relation_to_type": "type", "validated": true, "ani": 81.1628, "matched_fragments": 358, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium senegalense", "strain": "strain=Marseille-P4329", "accession": "GCA_900411315.1", "taxid": 2080750, "species_taxid": 2080750, "relation_to_type": "type", "validated": true, "ani": 80.9238, "matched_fragments": 387, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium haemomassiliense", "strain": "strain=Marseille-Q3615", "accession": "GCA_013978595.1", "taxid": 2754726, "species_taxid": 2754726, "relation_to_type": "type", "validated": true, "ani": 80.6571, "matched_fragments": 384, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium jeddahense", "strain": "strain=JCB", "accession": "GCA_000577555.1", "taxid": 1414719, "species_taxid": 1414719, "relation_to_type": "type", "validated": true, "ani": 80.4777, "matched_fragments": 353, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium ihumii", "strain": "strain=GD7", "accession": "GCA_000403725.2", "taxid": 1232427, "species_taxid": 1232427, "relation_to_type": "type", "validated": true, "ani": 80.3731, "matched_fragments": 357, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium afermentans subsp. lipophilum", "strain": "strain=CCUG 32105", "accession": "GCA_015351335.1", "taxid": 144184, "species_taxid": 38286, "relation_to_type": "type", "validated": true, "ani": 80.3236, "matched_fragments": 368, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium fournieri", "strain": "strain=Marseille-P2948", "accession": "GCA_900176865.1", "taxid": 1852390, "species_taxid": 1852390, "relation_to_type": "type", "validated": true, "ani": 80.1667, "matched_fragments": 356, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium lujinxingii", "strain": "strain=zg-917", "accession": "GCA_014490555.1", "taxid": 2763010, "species_taxid": 2763010, "relation_to_type": "type", "validated": true, "ani": 80.059, "matched_fragments": 366, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium bouchesdurhonense", "strain": "strain=SN14", "accession": "GCA_900078305.2", "taxid": 1720192, "species_taxid": 1720192, "relation_to_type": "type", "validated": true, "ani": 80.0501, "matched_fragments": 360, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium tuscaniense", "strain": "strain=CCUG 51321T", "accession": "GCA_008693065.1", "taxid": 302449, "species_taxid": 302449, "relation_to_type": "type", "validated": true, "ani": 80.0054, "matched_fragments": 323, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium marinum", "strain": "strain=CGMCC 1.6998", "accession": "GCA_014645275.1", "taxid": 349751, "species_taxid": 349751, "relation_to_type": "type", "validated": true, "ani": 79.7644, "matched_fragments": 310, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium marinum", "strain": "strain=DSM 44953", "accession": "GCA_000835165.1", "taxid": 349751, "species_taxid": 349751, "relation_to_type": "type", "validated": true, "ani": 79.66, "matched_fragments": 312, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium liangguodongii", "strain": "strain=2184", "accession": "GCA_003070865.1", "taxid": 2079535, "species_taxid": 2079535, "relation_to_type": "type", "validated": true, "ani": 79.0271, "matched_fragments": 307, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium striatum", "strain": "strain=FDAARGOS_1054", "accession": "GCA_016403285.1", "taxid": 43770, "species_taxid": 43770, "relation_to_type": "type", "validated": true, "ani": 78.3748, "matched_fragments": 161, "total_fragments": 729, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 99.54, "contamination": 0.52, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_900156665.1", "gtdb_species": "s__Corynebacterium appendicis", "ani": 100.0, "matched_fragments": 729, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_017942225.1", "gtdb_species": "s__Corynebacterium sp017942225", "ani": 87.9782, "matched_fragments": 604, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_900155535.1", "gtdb_species": "s__Corynebacterium urinipleomorphum", "ani": 85.1443, "matched_fragments": 581, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_000143825.1", "gtdb_species": "s__Corynebacterium genitalium_A", "ani": 81.4864, "matched_fragments": 471, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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": "GCA_900618065.1", "gtdb_species": "s__Corynebacterium sp900618065", "ani": 80.8576, "matched_fragments": 457, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_015351335.1", "gtdb_species": "s__Corynebacterium lipophilum", "ani": 80.2909, "matched_fragments": 370, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_900078305.2", "gtdb_species": "s__Corynebacterium bouchesdurhonense", "ani": 80.0741, "matched_fragments": 358, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008693065.1", "gtdb_species": "s__Corynebacterium tuscaniense", "ani": 80.0182, "matched_fragments": 323, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "98.40", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000835165.1", "gtdb_species": "s__Corynebacterium marinum", "ani": 79.66, "matched_fragments": 312, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000159135.1", "gtdb_species": "s__Corynebacterium striatum", "ani": 78.2404, "matched_fragments": 161, "total_fragments": 729, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 41, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.275, "cell_length": 0.068, "doubling_h": -0.089, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.292, "genome_size": 2237306.0, "gc_content": 59.791, "coding_genes": 2390.094, "rRNA16S_genes": 4.282, "tRNA_genes": 52.979, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.75, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.985, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.014, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Corynebacterium", "appendicis", "CIP", "107643" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }