{ "type": "genome", "identifier": "GCA_934233085.1", "organism": "uncultured Haemophilus sp.", "title": "uncultured Haemophilus sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "stanford university school of medicine", "publication": [ {} ], "properties": { "assembly_accession": "GCA_934233085.1", "bioproject": "PRJEB49206", "biosample": "SAMEA13512151", "wgs_master": "CAKQGM000000000.1", "refseq_category": "na", "taxid": "237779", "species_taxid": "237779", "organism_name": "uncultured Haemophilus sp.", "infraspecific_name": "", "isolate": "REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_E_4_1847.73", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/15", "asm_name": "ERR7745888_bin.73", "submitter": "stanford university school of medicine", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/934/233/085/GCA_934233085.1_ERR7745888_bin.73", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-04-15", "dateModified": "2022-04-15", "datePublished": "2022-04-15", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Haemophilus sp." ], "sample_taxid": [ "237779" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Tanzania" ], "sample_host_location_id": [], "data_size": "0.482 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 43.9, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1669338", "Number of Sequences": "287", "Longest Sequences (bp)": "32223", "N50 (bp)": "7440", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.7", "Number of CDSs": "1407", "Average Protein Length": "290.3", "Coding Ratio (%)": "73.4", "Number of rRNAs": "0", "Number of tRNAs": "11", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Haemophilus paraphrohaemolyticus", "strain": "strain=CCUG 3718", "accession": "GCA_002015045.1", "taxid": 736, "species_taxid": 736, "relation_to_type": "type", "validated": true, "ani": 95.0482, "matched_fragments": 359, "total_fragments": 395, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Haemophilus parahaemolyticus", "strain": "strain=FDAARGOS_1199", "accession": "GCA_016889385.1", "taxid": 735, "species_taxid": 735, "relation_to_type": "type", "validated": true, "ani": 89.773, "matched_fragments": 321, "total_fragments": 395, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus parahaemolyticus", "strain": "strain=NCTC 8479", "accession": "GCA_900450675.1", "taxid": 735, "species_taxid": 735, "relation_to_type": "type", "validated": true, "ani": 89.748, "matched_fragments": 325, "total_fragments": 395, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus parahaemolyticus", "strain": "strain=CCUG 3716", "accession": "GCA_002015035.1", "taxid": 735, "species_taxid": 735, "relation_to_type": "type", "validated": true, "ani": 89.7034, "matched_fragments": 324, "total_fragments": 395, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus parahaemolyticus", "strain": "strain=HK385", "accession": "GCA_000262265.1", "taxid": 735, "species_taxid": 735, "relation_to_type": "type", "validated": true, "ani": 89.6269, "matched_fragments": 325, "total_fragments": 395, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus sputorum", "strain": "strain=CCUG 13788", "accession": "GCA_000238795.2", "taxid": 1078480, "species_taxid": 1078480, "relation_to_type": "type", "validated": true, "ani": 78.3173, "matched_fragments": 155, "total_fragments": 395, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 43.9, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002015045.1", "gtdb_species": "s__Haemophilus_A paraphrohaemolyticus", "ani": 95.0482, "matched_fragments": 359, "total_fragments": 395, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.72", "min_intra_species_ani": "95.26", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCF_002015035.1", "gtdb_species": "s__Haemophilus_A parahaemolyticus", "ani": 89.7657, "matched_fragments": 322, "total_fragments": 395, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.50", "min_intra_species_ani": "95.62", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.88", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCA_018373095.1", "gtdb_species": "s__Haemophilus_A parahaemolyticus_A", "ani": 88.7926, "matched_fragments": 295, "total_fragments": 395, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_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_003101015.1", "gtdb_species": "s__Actinobacillus_A porcitonsillarum", "ani": 78.9764, "matched_fragments": 161, "total_fragments": 395, "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_000175195.1", "gtdb_species": "s__Actinobacillus_A minor", "ani": 78.7266, "matched_fragments": 159, "total_fragments": 395, "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_000238795.1", "gtdb_species": "s__Haemophilus_A sputorum", "ani": 78.3004, "matched_fragments": 155, "total_fragments": 395, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.57", "min_intra_species_ani": "96.93", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_014541205.1", "gtdb_species": "s__Mannheimia bovis", "ani": 77.9501, "matched_fragments": 129, "total_fragments": 395, "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_901687125.1", "gtdb_species": "s__Actinobacillus vicugnae", "ani": 77.7359, "matched_fragments": 146, "total_fragments": 395, "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_013377235.1", "gtdb_species": "s__Mannheimia varigena", "ani": 77.6142, "matched_fragments": 134, "total_fragments": 395, "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": "GCA_002002485.1", "gtdb_species": "s__GCF-002002485 sp002002485", "ani": 77.4795, "matched_fragments": 101, "total_fragments": 395, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__GCF-002002485", "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_011455275.1", "gtdb_species": "s__Frederiksenia sp011455275", "ani": 77.3337, "matched_fragments": 93, "total_fragments": 395, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia", "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_002015115.1", "gtdb_species": "s__Haemophilus_E paracuniculus", "ani": 77.1644, "matched_fragments": 106, "total_fragments": 395, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_E", "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_013377995.1", "gtdb_species": "s__Mannheimia pernigra", "ani": 77.0792, "matched_fragments": 118, "total_fragments": 395, "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_004345745.1", "gtdb_species": "s__Nicoletella semolina", "ani": 75.9654, "matched_fragments": 59, "total_fragments": 395, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Nicoletella", "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": -0.481, "cell_length": 0.012, "doubling_h": -0.018, "growth_tmp": 36.571, "optimum_tmp": 36.436, "optimum_ph": 6.75, "genome_size": 2054106.422, "gc_content": 39.271, "coding_genes": 1822.685, "rRNA16S_genes": 6.018, "tRNA_genes": 56.355, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 0.23, "anaerobic_respiration": 0.076, "aerobic_respiration": 0.692, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Enterobacterales", "f__Pasteurellaceae", "g__Haemophilus_A", "s__Haemophilus_A paraphrohaemolyticus_A" ], "_genome_taxon": [ "uncultured", "Haemophilus", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Enterobacterales", "f__Pasteurellaceae", "g__Haemophilus_A", "s__Haemophilus_A paraphrohaemolyticus_A", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Enterobacterales", "Pasteurellaceae", "Haemophilus", "A", "Haemophilus", "A", "paraphrohaemolyticus", "A" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }