{ "type": "genome", "identifier": "GCA_903829095.1", "organism": "uncultured proteobacterium", "title": "uncultured proteobacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "BILS", "publication": [ {} ], "properties": { "assembly_accession": "GCA_903829095.1", "bioproject": "PRJEB38681", "biosample": "SAMEA6943525", "wgs_master": "CAIKOT000000000.1", "refseq_category": "na", "taxid": "153809", "species_taxid": "153809", "organism_name": "uncultured proteobacterium", "infraspecific_name": "", "isolate": "MJ-2014-D1_bin-0531", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/18", "asm_name": "freshwater MAG --- MJ-2014-D1_bin-0531", "submitter": "BILS", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/829/095/GCA_903829095.1_freshwater_MAG_---_MJ-2014-D1_bin-0531", "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": "2020-07-18", "dateModified": "2020-07-18", "datePublished": "2020-07-18", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured proteobacterium" ], "sample_taxid": [ "153809" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Finland" ], "sample_host_location_id": [], "data_size": "0.811 MB", "sample_ph_range": { "min": 57.0, "max": 57.0 }, "sample_temperature_range": { "min": 142.0, "max": 142.0 }, "completeness": 62.5, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2844581", "Number of Sequences": "99", "Longest Sequences (bp)": "189910", "N50 (bp)": "46409", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.1", "Number of CDSs": "2602", "Average Protein Length": "313.9", "Coding Ratio (%)": "86.1", "Number of rRNAs": "3", "Number of tRNAs": "36", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylomonas denitrificans", "strain": "strain=FJG1", "accession": "GCA_000785705.2", "taxid": 1538553, "species_taxid": 1538553, "relation_to_type": "type", "validated": true, "ani": 77.4396, "matched_fragments": 194, "total_fragments": 899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomonas albis", "strain": "strain=EbA", "accession": "GCA_014850955.1", "taxid": 1854563, "species_taxid": 1854563, "relation_to_type": "type", "validated": true, "ani": 77.3269, "matched_fragments": 189, "total_fragments": 899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomonas koyamae", "strain": "strain=JCM 16701", "accession": "GCA_001312005.1", "taxid": 702114, "species_taxid": 702114, "relation_to_type": "suspected-type", "validated": true, "ani": 76.8107, "matched_fragments": 138, "total_fragments": 899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomonas koyamae", "strain": "strain=Fw12E-Y", "accession": "GCA_019669905.1", "taxid": 702114, "species_taxid": 702114, "relation_to_type": "suspected-type", "validated": true, "ani": 76.7873, "matched_fragments": 146, "total_fragments": 899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomonas rhizoryzae", "strain": "strain=GJ1", "accession": "GCA_008632455.1", "taxid": 2608981, "species_taxid": 2608981, "relation_to_type": "type", "validated": true, "ani": 76.6792, "matched_fragments": 94, "total_fragments": 899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crenothrix polyspora", "strain": "", "accession": "GCA_900163755.1", "taxid": 360316, "species_taxid": 360316, "relation_to_type": "reftype", "validated": true, "ani": 76.3418, "matched_fragments": 71, "total_fragments": 899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylovulum miyakonense", "strain": "strain=HT12", "accession": "GCA_000384075.1", "taxid": 645578, "species_taxid": 645578, "relation_to_type": "type", "validated": true, "ani": 76.3228, "matched_fragments": 85, "total_fragments": 899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomarinum vadi", "strain": "strain=IT-4", "accession": "GCA_000733935.1", "taxid": 438855, "species_taxid": 438855, "relation_to_type": "type", "validated": true, "ani": 76.2481, "matched_fragments": 65, "total_fragments": 899, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 62.5, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903918375.1", "gtdb_species": "s__Methylomonas sp903918375", "ani": 99.8825, "matched_fragments": 848, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.06", "min_intra_species_ani": "95.20", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.72", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCA_903931355.1", "gtdb_species": "s__Methylomonas sp903931355", "ani": 90.8978, "matched_fragments": 419, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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_903902945.1", "gtdb_species": "s__Methylomonas sp903902945", "ani": 77.8524, "matched_fragments": 214, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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_001644035.1", "gtdb_species": "s__Methylomonas methanica_A", "ani": 77.8522, "matched_fragments": 205, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.96", "min_intra_species_ani": "95.96", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002928965.1", "gtdb_species": "s__Methylomonas sp002928965", "ani": 77.7642, "matched_fragments": 162, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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_009925045.1", "gtdb_species": "s__Methylomonas sp009925045", "ani": 77.711, "matched_fragments": 109, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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_001644045.1", "gtdb_species": "s__Methylomonas methanica", "ani": 77.491, "matched_fragments": 192, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_002083615.1", "gtdb_species": "s__Methylomonas sp002083615", "ani": 77.4904, "matched_fragments": 166, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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_001644015.1", "gtdb_species": "s__Methylomonas lenta", "ani": 77.4247, "matched_fragments": 166, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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_000214665.1", "gtdb_species": "s__Methylomonas methanica_B", "ani": 77.416, "matched_fragments": 142, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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_903858105.1", "gtdb_species": "s__Methylomonas sp903858105", "ani": 77.3661, "matched_fragments": 155, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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_903064715.1", "gtdb_species": "s__Methylomonas sp903064715", "ani": 77.3269, "matched_fragments": 189, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "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_000515215.1", "gtdb_species": "s__Methylomonas sp000515215", "ani": 77.3172, "matched_fragments": 205, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.46", "min_intra_species_ani": "95.46", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_903928685.1", "gtdb_species": "s__Methylovulum sp903928685", "ani": 76.7498, "matched_fragments": 124, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.86", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_018734325.1", "gtdb_species": "s__Methylomonas paludis", "ani": 76.7394, "matched_fragments": 139, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "98.96", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000384075.1", "gtdb_species": "s__Methylovulum miyakonense", "ani": 76.3278, "matched_fragments": 85, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.67", "min_intra_species_ani": "96.67", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000733935.1", "gtdb_species": "s__Methylomarinum vadi", "ani": 76.261, "matched_fragments": 67, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomarinum", "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_903863905.1", "gtdb_species": "s__KS41 sp903863905", "ani": 76.164, "matched_fragments": 54, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.63", "min_intra_species_ani": "99.29", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 33, "status": "-" }, { "accession": "GCA_005239965.1", "gtdb_species": "s__Crenothrix sp005239965", "ani": 76.0074, "matched_fragments": 51, "total_fragments": 899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Crenothrix", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Methylococcales", "f__Methylomonadaceae", "g__Methylomonas", "s__Methylomonas sp903918375" ], "_genome_taxon": [ "uncultured", "proteobacterium", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Methylococcales", "f__Methylomonadaceae", "g__Methylomonas", "s__Methylomonas sp903918375", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Methylococcales", "Methylomonadaceae", "Methylomonas", "Methylomonas", "sp903918375" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }