{ "type": "genome", "identifier": "GCA_020442175.1", "organism": "Hyphomicrobiaceae bacterium", "title": "Hyphomicrobiaceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "The University Hong Kong", "publication": [ {} ], "properties": { "assembly_accession": "GCA_020442175.1", "bioproject": "PRJNA432264", "biosample": "SAMN14564356", "wgs_master": "JAGRKT000000000.1", "refseq_category": "na", "taxid": "2015799", "species_taxid": "2015799", "organism_name": "Hyphomicrobiaceae bacterium", "infraspecific_name": "", "isolate": "HKST-UBA46", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/10/12", "asm_name": "ASM2044217v1", "submitter": "The University Hong Kong", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/442/175/GCA_020442175.1_ASM2044217v1", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-10-12", "dateModified": "2021-10-12", "datePublished": "2021-10-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Hyphomicrobiaceae bacterium" ], "sample_taxid": [ "2015799" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Hong Kong SAR, Shatin waste water treatment plant" ], "sample_host_location_id": [], "data_size": "1.092 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 92.21, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3824151", "Number of Sequences": "418", "Longest Sequences (bp)": "41719", "N50 (bp)": "14035", "Gap Ratio (%)": "0.241230", "GCcontent (%)": "56.7", "Number of CDSs": "3188", "Average Protein Length": "305.4", "Coding Ratio (%)": "76.4", "Number of rRNAs": "0", "Number of tRNAs": "31", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Hyphomicrobium nitrativorans", "strain": "strain=NL23", "accession": "GCA_000503895.1", "taxid": 1427356, "species_taxid": 1427356, "relation_to_type": "type", "validated": true, "ani": 76.1723, "matched_fragments": 70, "total_fragments": 1057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomicrobium zavarzinii", "strain": "strain=ZV-622", "accession": "GCA_000383415.1", "taxid": 48292, "species_taxid": 48292, "relation_to_type": "type", "validated": true, "ani": 76.083, "matched_fragments": 67, "total_fragments": 1057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomicrobium denitrificans", "strain": "strain=ATCC 51888", "accession": "GCA_000143145.1", "taxid": 53399, "species_taxid": 53399, "relation_to_type": "type", "validated": true, "ani": 75.8962, "matched_fragments": 59, "total_fragments": 1057, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 92.21, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_016793635.1", "gtdb_species": "s__JAEUMD01 sp016793635", "ani": 76.4185, "matched_fragments": 119, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__JAEUMD01", "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_019137195.1", "gtdb_species": "s__Hyphomicrobium sp019137195", "ani": 76.1801, "matched_fragments": 58, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium", "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_000503895.1", "gtdb_species": "s__Hyphomicrobium nitrativorans", "ani": 76.1723, "matched_fragments": 70, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium", "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_016793445.1", "gtdb_species": "s__Hyphomicrobium sp016793445", "ani": 76.0608, "matched_fragments": 66, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium", "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_001516065.1", "gtdb_species": "s__Filomicrobium sp001516065", "ani": 75.9758, "matched_fragments": 67, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium", "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_018819265.1", "gtdb_species": "s__Filomicrobium sp018819265", "ani": 75.9549, "matched_fragments": 87, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium", "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_011330955.1", "gtdb_species": "s__DSSY01 sp011330955", "ani": 75.9232, "matched_fragments": 53, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__DSSY01", "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_000143145.1", "gtdb_species": "s__Hyphomicrobium denitrificans", "ani": 75.9186, "matched_fragments": 58, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.20", "min_intra_species_ani": "95.20", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_011046675.1", "gtdb_species": "s__AWTP1-13 sp011046675", "ani": 75.9005, "matched_fragments": 61, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13", "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_003963125.1", "gtdb_species": "s__AWTP1-13 sp003963125", "ani": 75.8891, "matched_fragments": 54, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13", "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_900117455.1", "gtdb_species": "s__Hyphomicrobium sp900117455", "ani": 75.8571, "matched_fragments": 71, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium", "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_009026145.1", "gtdb_species": "s__Hyphomicrobium_A sp009026145", "ani": 75.7969, "matched_fragments": 86, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_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": "GCA_003987725.1", "gtdb_species": "s__Hyphomicrobium sp003987725", "ani": 75.7409, "matched_fragments": 65, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017304275.1", "gtdb_species": "s__Hyphomicrobium sp017304275", "ani": 75.6509, "matched_fragments": 57, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium", "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_008933705.1", "gtdb_species": "s__AWTP1-13 sp008933705", "ani": 75.6306, "matched_fragments": 66, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13", "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_018242295.1", "gtdb_species": "s__Hyphomicrobium sp018242295", "ani": 75.6161, "matched_fragments": 56, "total_fragments": 1057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.15", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.162, "cell_length": 0.227, "doubling_h": null, "growth_tmp": 28.511, "optimum_tmp": 29.342, "optimum_ph": 7.344, "genome_size": 4094362.09, "gc_content": 60.93, "coding_genes": 3558.106, "rRNA16S_genes": 1.75, "tRNA_genes": 46.266, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.92, "range_salinity": 0.0, "facultative_respiration": 0.125, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.875, "mesophilic_range_tmp": 0.666, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.333, "bacillus_cell_shape": 0.916, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.083, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Hyphomicrobiaceae", "g__JAEUMD01", "s__JAEUMD01 sp020638055" ], "_genome_taxon": [ "Hyphomicrobiaceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Hyphomicrobiaceae", "g__JAEUMD01", "s__JAEUMD01 sp020638055", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhizobiales", "Hyphomicrobiaceae", "JAEUMD01", "JAEUMD01", "sp020638055" ], "_meo": [ { "id": "MEO_0000014", "label": "activated sludge" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }