{ "type": "genome", "identifier": "GCF_004342115.1", "organism": "Mannheimia haemolytica", "title": "Mannheimia haemolytica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004342115.1", "bioproject": "PRJNA224116", "biosample": "SAMN10363427", "wgs_master": "SMAC00000000.1", "refseq_category": "na", "taxid": "75985", "species_taxid": "75985", "organism_name": "Mannheimia haemolytica", "infraspecific_name": "strain=DSM 10531", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/11", "asm_name": "ASM434211v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004342115.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/342/115/GCF_004342115.1_ASM434211v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2583665", "genome_size_ungapped": "2583569", "gc_percent": "41.000000", "replicon_count": "0", "scaffold_count": "71", "contig_count": "71", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004342115.1-RS_2024_04_17", "annotation_date": "2024-04-17", "total_gene_count": "2657", "protein_coding_gene_count": "2519", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-11", "dateModified": "2019-03-11", "datePublished": "2019-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Mannheimia haemolytica" ], "sample_taxid": [ "75985" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Pennsylvania" ], "sample_host_location_id": [], "data_size": "0.733 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)": "2583665", "Number of Sequences": "71", "Longest Sequences (bp)": "140937", "N50 (bp)": "78910", "Gap Ratio (%)": "0.003909", "GCcontent (%)": "41.1", "Number of CDSs": "2586", "Average Protein Length": "295.8", "Coding Ratio (%)": "88.8", "Number of rRNAs": "4", "Number of tRNAs": "56", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mannheimia haemolytica", "strain": "strain=DSM 10531", "accession": "GCA_004342115.1", "taxid": 75985, "species_taxid": 75985, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 822, "total_fragments": 826, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mannheimia haemolytica", "strain": "strain=NCTC9380", "accession": "GCA_900452985.1", "taxid": 75985, "species_taxid": 75985, "relation_to_type": "type", "validated": true, "ani": 99.9988, "matched_fragments": 826, "total_fragments": 826, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mannheimia ovis", "strain": "strain=ZY170218", "accession": "GCA_009828705.1", "taxid": 2679994, "species_taxid": 2679994, "relation_to_type": "type", "validated": true, "ani": 83.645, "matched_fragments": 516, "total_fragments": 826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mannheimia bovis", "strain": "strain=ZY190616", "accession": "GCA_014541205.1", "taxid": 2770636, "species_taxid": 2770636, "relation_to_type": "type", "validated": true, "ani": 82.7517, "matched_fragments": 545, "total_fragments": 826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mannheimia varigena", "strain": "strain=177", "accession": "GCA_013377235.1", "taxid": 85404, "species_taxid": 85404, "relation_to_type": "type", "validated": true, "ani": 82.7113, "matched_fragments": 558, "total_fragments": 826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mannheimia pernigra", "strain": "strain=17CN0883", "accession": "GCA_013377995.1", "taxid": 111844, "species_taxid": 111844, "relation_to_type": "type", "validated": true, "ani": 82.0181, "matched_fragments": 493, "total_fragments": 826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mannheimia granulomatis", "strain": "strain=DSM 19156", "accession": "GCA_000621105.1", "taxid": 85402, "species_taxid": 85402, "relation_to_type": "type", "validated": true, "ani": 81.2995, "matched_fragments": 540, "total_fragments": 826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinobacillus equuli", "strain": "strain=NCTC8529", "accession": "GCA_900636745.1", "taxid": 718, "species_taxid": 718, "relation_to_type": "type", "validated": true, "ani": 79.1195, "matched_fragments": 316, "total_fragments": 826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinobacillus capsulatus", "strain": "strain=DSM 19761", "accession": "GCA_000374285.1", "taxid": 717, "species_taxid": 717, "relation_to_type": "type", "validated": true, "ani": 79.0398, "matched_fragments": 302, "total_fragments": 826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinobacillus pleuropneumoniae", "strain": "strain=4074", "accession": "GCA_000167095.1", "taxid": 715, "species_taxid": 715, "relation_to_type": "type", "validated": true, "ani": 78.7668, "matched_fragments": 278, "total_fragments": 826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Haemophilus] ducreyi", "strain": "strain=CIP 54.2", "accession": "GCA_001043455.1", "taxid": 730, "species_taxid": 730, "relation_to_type": "type", "validated": true, "ani": 78.0811, "matched_fragments": 153, "total_fragments": 826, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004342115.1", "gtdb_species": "s__Mannheimia haemolytica", "ani": 100.0, "matched_fragments": 822, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "95.33", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.85", "num_clustered_genomes": 196, "status": "conclusive" }, { "accession": "GCF_000521605.1", "gtdb_species": "s__Mannheimia sp000521605", "ani": 83.1806, "matched_fragments": 576, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia", "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_014541205.1", "gtdb_species": "s__Mannheimia bovis", "ani": 82.7517, "matched_fragments": 545, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia", "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_013377235.1", "gtdb_species": "s__Mannheimia varigena", "ani": 82.7113, "matched_fragments": 558, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.47", "min_intra_species_ani": "97.09", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_013377995.1", "gtdb_species": "s__Mannheimia pernigra", "ani": 82.0179, "matched_fragments": 493, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "97.60", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_011455695.1", "gtdb_species": "s__Mannheimia granulomatis_A", "ani": 81.4112, "matched_fragments": 492, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia", "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_013377255.1", "gtdb_species": "s__Mannheimia granulomatis", "ani": 81.3736, "matched_fragments": 539, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.35", "min_intra_species_ani": "95.73", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000175195.1", "gtdb_species": "s__Actinobacillus_A minor", "ani": 79.2087, "matched_fragments": 270, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_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": "-" }, { "accession": "GCF_000188255.1", "gtdb_species": "s__Actinobacillus ureae", "ani": 79.1761, "matched_fragments": 285, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "99.21", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900636745.1", "gtdb_species": "s__Actinobacillus equuli", "ani": 79.1045, "matched_fragments": 317, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.82", "min_intra_species_ani": "97.64", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003101015.1", "gtdb_species": "s__Actinobacillus_A porcitonsillarum", "ani": 79.0934, "matched_fragments": 276, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.10", "min_intra_species_ani": "97.10", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000739435.1", "gtdb_species": "s__Actinobacillus suis", "ani": 79.0878, "matched_fragments": 311, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.85", "min_intra_species_ani": "99.75", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.94", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000374285.1", "gtdb_species": "s__Actinobacillus capsulatus", "ani": 79.0544, "matched_fragments": 301, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus", "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_900109315.1", "gtdb_species": "s__Haemophilus_B ducreyi", "ani": 78.0536, "matched_fragments": 153, "total_fragments": 826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 31, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.3, "genome_size": 2608049.139, "gc_content": 41.029, "coding_genes": 2581.731, "rRNA16S_genes": 6.0, "tRNA_genes": 63.312, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Mannheimia", "haemolytica" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }