{ "type": "genome", "identifier": "GCF_019633665.1", "organism": "Pasteurella testudinis DSM 23072", "title": "Pasteurella testudinis DSM 23072", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019633665.1", "bioproject": "PRJNA224116", "biosample": "SAMN02850906", "wgs_master": "JNUW00000000.1", "refseq_category": "na", "taxid": "1122938", "species_taxid": "761", "organism_name": "Pasteurella testudinis DSM 23072", "infraspecific_name": "strain=DSM 23072", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/08/16", "asm_name": "ASM1963366v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_019633665.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/633/665/GCF_019633665.1_ASM1963366v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2917405", "genome_size_ungapped": "2915576", "gc_percent": "47.500000", "replicon_count": "0", "scaffold_count": "68", "contig_count": "71", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-08", "total_gene_count": "2841", "protein_coding_gene_count": "2737", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-08-16", "dateModified": "2021-08-16", "datePublished": "2021-08-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Pasteurella testudinis DSM 23072" ], "sample_taxid": [ "1122938" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.824 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)": "2917405", "Number of Sequences": "68", "Longest Sequences (bp)": "351884", "N50 (bp)": "101063", "Gap Ratio (%)": "0.064372", "GCcontent (%)": "47.3", "Number of CDSs": "2724", "Average Protein Length": "312.3", "Coding Ratio (%)": "87.5", "Number of rRNAs": "4", "Number of tRNAs": "46", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pasteurella testudinis", "strain": "strain=DSM 23072", "accession": "GCA_019633665.1", "taxid": 761, "species_taxid": 761, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 934, "total_fragments": 937, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pasteurella testudinis", "strain": "strain=DSM 23072", "accession": "GCA_900176075.1", "taxid": 761, "species_taxid": 761, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 934, "total_fragments": 937, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pasteurella testudinis", "strain": "strain=NCTC12150", "accession": "GCA_900454705.1", "taxid": 761, "species_taxid": 761, "relation_to_type": "type", "validated": true, "ani": 99.9933, "matched_fragments": 935, "total_fragments": 937, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Testudinibacter aquarius", "strain": "strain=ELNT2X", "accession": "GCA_009761355.1", "taxid": 1524974, "species_taxid": 1524974, "relation_to_type": "type", "validated": true, "ani": 82.3526, "matched_fragments": 606, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Testudinibacter aquarius", "strain": "strain=DSM 28140", "accession": "GCA_004342725.1", "taxid": 1524974, "species_taxid": 1524974, "relation_to_type": "type", "validated": true, "ani": 82.3422, "matched_fragments": 612, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirabiliibacterium mucosae", "strain": "strain=20609_3", "accession": "GCA_014884965.1", "taxid": 28156, "species_taxid": 28156, "relation_to_type": "type", "validated": true, "ani": 77.5402, "matched_fragments": 185, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=DSM 16636", "accession": "GCA_021278985.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 75.7343, "matched_fragments": 70, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900176075.1", "gtdb_species": "s__Chelonobacter testudinis", "ani": 100.0, "matched_fragments": 934, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter", "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_004342725.1", "gtdb_species": "s__Chelonobacter aquarius", "ani": 82.357, "matched_fragments": 611, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.20", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCA_006228005.1", "gtdb_species": "s__Chelonobacter sp006228005", "ani": 82.2785, "matched_fragments": 557, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "99.87", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000772535.1", "gtdb_species": "s__Chelonobacter oris", "ani": 80.5122, "matched_fragments": 561, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter", "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_014884995.1", "gtdb_species": "s__Spirabiliibacterium pneumoniae", "ani": 77.9038, "matched_fragments": 149, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium", "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_014884965.1", "gtdb_species": "s__Spirabiliibacterium mucosae", "ani": 77.5706, "matched_fragments": 184, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.18", "min_intra_species_ani": "96.18", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_000752995.2", "gtdb_species": "s__Necropsobacter massiliensis_B", "ani": 77.4812, "matched_fragments": 180, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter", "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_004363295.1", "gtdb_species": "s__Mesocricetibacter intestinalis", "ani": 77.4175, "matched_fragments": 130, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mesocricetibacter", "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_017160915.1", "gtdb_species": "s__Aggregatibacter actinomycetemcomitans_B", "ani": 77.3033, "matched_fragments": 189, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter", "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_000379785.1", "gtdb_species": "s__Gallibacterium anatis", "ani": 77.223, "matched_fragments": 96, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Gallibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.46", "min_intra_species_ani": "96.89", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.80", "num_clustered_genomes": 28, "status": "-" }, { "accession": "GCA_900454475.1", "gtdb_species": "s__Actinobacillus_B mairii", "ani": 77.1141, "matched_fragments": 113, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B", "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_006438725.1", "gtdb_species": "s__Ewingella americana_A", "ani": 76.0189, "matched_fragments": 52, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella", "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": -0.222, "cell_length": -0.222, "doubling_h": 0.0, "growth_tmp": 35.703, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2204817.066, "gc_content": 38.937, "coding_genes": 2049.235, "rRNA16S_genes": 6.0, "tRNA_genes": 55.427, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pasteurella", "testudinis", "DSM", "23072" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }