{ "type": "genome", "identifier": "GCF_003002015.1", "organism": "Pontibacter ummariensis", "title": "Pontibacter ummariensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003002015.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621255", "wgs_master": "PVZE00000000.1", "refseq_category": "na", "taxid": "1610492", "species_taxid": "1610492", "organism_name": "Pontibacter ummariensis", "infraspecific_name": "strain=NKM1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/15", "asm_name": "ASM300201v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003002015.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/002/015/GCF_003002015.1_ASM300201v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5965912", "genome_size_ungapped": "5965898", "gc_percent": "50.500000", "replicon_count": "0", "scaffold_count": "81", "contig_count": "81", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003002015.1-RS_2024_09_05", "annotation_date": "2024-09-05", "total_gene_count": "5088", "protein_coding_gene_count": "4997", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-15", "dateModified": "2018-03-15", "datePublished": "2018-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Pontibacter ummariensis" ], "sample_taxid": [ "1610492" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.709 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)": "5965912", "Number of Sequences": "81", "Longest Sequences (bp)": "465508", "N50 (bp)": "202082", "Gap Ratio (%)": "0.000235", "GCcontent (%)": "50.3", "Number of CDSs": "4984", "Average Protein Length": "334.6", "Coding Ratio (%)": "83.9", "Number of rRNAs": "0", "Number of tRNAs": "41", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pontibacter ummariensis", "strain": "strain=NKM1", "accession": "GCA_003002015.1", "taxid": 1610492, "species_taxid": 1610492, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1943, "total_fragments": 1946, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pontibacter ummariensis", "strain": "strain=NKM1", "accession": "GCA_900188175.1", "taxid": 1610492, "species_taxid": 1610492, "relation_to_type": "type", "validated": true, "ani": 99.9987, "matched_fragments": 1943, "total_fragments": 1946, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pontibacter actiniarum", "strain": "strain=DSM 19842", "accession": "GCA_003585765.1", "taxid": 323450, "species_taxid": 323450, "relation_to_type": "type", "validated": true, "ani": 79.3475, "matched_fragments": 637, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter actiniarum", "strain": "strain=DSM 19842", "accession": "GCA_000472485.1", "taxid": 323450, "species_taxid": 323450, "relation_to_type": "type", "validated": true, "ani": 79.2747, "matched_fragments": 637, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter mangrovi", "strain": "strain=HB172049", "accession": "GCA_006385705.1", "taxid": 2589816, "species_taxid": 2589816, "relation_to_type": "type", "validated": true, "ani": 78.8451, "matched_fragments": 574, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter korlensis", "strain": "strain=X14-1T", "accession": "GCA_000973725.1", "taxid": 400092, "species_taxid": 400092, "relation_to_type": "type", "validated": true, "ani": 78.6711, "matched_fragments": 449, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter mucosus", "strain": "strain=DSM 100162", "accession": "GCA_003054055.1", "taxid": 1649266, "species_taxid": 1649266, "relation_to_type": "type", "validated": true, "ani": 78.6695, "matched_fragments": 545, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter flavimaris", "strain": "strain=S10-8", "accession": "GCA_001907195.1", "taxid": 1797110, "species_taxid": 1797110, "relation_to_type": "type", "validated": true, "ani": 78.4313, "matched_fragments": 536, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter chinhatensis", "strain": "strain=LP51", "accession": "GCA_900113285.1", "taxid": 1436961, "species_taxid": 1436961, "relation_to_type": "type", "validated": true, "ani": 78.4013, "matched_fragments": 511, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter ruber", "strain": "strain=JC213", "accession": "GCA_023630205.1", "taxid": 1343895, "species_taxid": 1343895, "relation_to_type": "type", "validated": true, "ani": 78.1573, "matched_fragments": 429, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter aquaedesilientis", "strain": "strain=JH31", "accession": "GCA_014773225.1", "taxid": 2766980, "species_taxid": 2766980, "relation_to_type": "type", "validated": true, "ani": 77.8502, "matched_fragments": 331, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter deserti", "strain": "strain=JC215", "accession": "GCA_023630255.1", "taxid": 1343896, "species_taxid": 1343896, "relation_to_type": "type", "validated": true, "ani": 77.5893, "matched_fragments": 301, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter silvestris", "strain": "strain=XAAS-R86T", "accession": "GCA_020907275.1", "taxid": 2305183, "species_taxid": 2305183, "relation_to_type": "type", "validated": true, "ani": 77.5685, "matched_fragments": 277, "total_fragments": 1946, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900188175.1", "gtdb_species": "s__Pontibacter ummariensis", "ani": 99.9987, "matched_fragments": 1943, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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": "conclusive" }, { "accession": "GCF_003585765.1", "gtdb_species": "s__Pontibacter actiniarum", "ani": 79.3439, "matched_fragments": 638, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_006385705.1", "gtdb_species": "s__Pontibacter sp006385705", "ani": 78.8675, "matched_fragments": 571, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_003054055.1", "gtdb_species": "s__Pontibacter mucosus", "ani": 78.6907, "matched_fragments": 542, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_000973725.1", "gtdb_species": "s__Pontibacter korlensis", "ani": 78.6528, "matched_fragments": 451, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_001907195.1", "gtdb_species": "s__Pontibacter sp001907195", "ani": 78.4241, "matched_fragments": 537, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_001611675.1", "gtdb_species": "s__Pontibacter akesuensis", "ani": 78.4074, "matched_fragments": 503, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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": 3, "status": "-" }, { "accession": "GCF_900113285.1", "gtdb_species": "s__Pontibacter chinhatensis", "ani": 78.4037, "matched_fragments": 512, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_003576375.1", "gtdb_species": "s__Pontibacter oryzae", "ani": 78.3874, "matched_fragments": 430, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_003367245.1", "gtdb_species": "s__Pontibacter diazotrophicus", "ani": 78.3441, "matched_fragments": 607, "total_fragments": 1946, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_009931655.1", "gtdb_species": "s__Pontibacter russatus", "ani": 78.1197, "matched_fragments": 517, "total_fragments": 1946, "gtdb_taxonomy": 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"coding_genes": 4209.666, "rRNA16S_genes": 4.0, "tRNA_genes": 46.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.363, "range_salinity": null, "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": 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 }, "_genome_taxon": [ "Pontibacter", "ummariensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }