{ "type": "genome", "identifier": "GCF_900113285.1", "organism": "Pontibacter chinhatensis", "title": "Pontibacter chinhatensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900113285.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421739", "wgs_master": "FOOT00000000.1", "refseq_category": "reference genome", "taxid": "1436961", "species_taxid": "1436961", "organism_name": "Pontibacter chinhatensis", "infraspecific_name": "strain=LP51", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2671180224 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900113285.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/113/285/GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5072663", "genome_size_ungapped": "5072663", "gc_percent": "52.000000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900113285.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "4279", "protein_coding_gene_count": "4222", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Pontibacter chinhatensis" ], "sample_taxid": [ "1436961" ], "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": "1.443 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5072663", "Number of Sequences": "25", "Longest Sequences (bp)": "1280063", "N50 (bp)": "638343", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.0", "Number of CDSs": "4213", "Average Protein Length": "338.4", "Coding Ratio (%)": "84.3", "Number of rRNAs": "3", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pontibacter chinhatensis", "strain": "strain=LP51", "accession": "GCA_900113285.1", "taxid": 1436961, "species_taxid": 1436961, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1674, "total_fragments": 1676, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pontibacter mucosus", "strain": "strain=DSM 100162", "accession": "GCA_003054055.1", "taxid": 1649266, "species_taxid": 1649266, "relation_to_type": "type", "validated": true, "ani": 92.0328, "matched_fragments": 1473, "total_fragments": 1676, "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": 83.3023, "matched_fragments": 1166, "total_fragments": 1676, "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": 81.6894, "matched_fragments": 997, "total_fragments": 1676, "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": 80.16, "matched_fragments": 806, "total_fragments": 1676, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter oryzae", "strain": "strain=KIRAN", "accession": "GCA_003576375.1", "taxid": 2304593, "species_taxid": 2304593, "relation_to_type": "type", "validated": true, "ani": 79.4579, "matched_fragments": 630, "total_fragments": 1676, "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": 79.1466, "matched_fragments": 741, 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"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": 77.6737, "matched_fragments": 201, "total_fragments": 1676, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900113285.1", "gtdb_species": "s__Pontibacter chinhatensis", "ani": 100.0, "matched_fragments": 1674, "total_fragments": 1676, "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": "conclusive" }, { "accession": "GCF_003054055.1", "gtdb_species": "s__Pontibacter 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"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": 79.1399, "matched_fragments": 744, "total_fragments": 1676, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.236, "cell_length": 0.229, "doubling_h": null, "growth_tmp": 28.5, "optimum_tmp": 29.924, "optimum_ph": 7.3, "genome_size": 5072663.0, "gc_content": 51.009, 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