{ "type": "genome", "identifier": "GCF_004005945.1", "organism": "Rheinheimera riviphila", "title": "Rheinheimera riviphila", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Kaohsiung University of Science and Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004005945.1", "bioproject": "PRJNA224116", "biosample": "SAMN10685512", "wgs_master": "SACS00000000.1", "refseq_category": "reference genome", "taxid": "1834037", "species_taxid": "1834037", "organism_name": "Rheinheimera riviphila", "infraspecific_name": "strain=KYPC3", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/01/08", "asm_name": "ASM400594v1", "asm_submitter": "National Kaohsiung University of Science and Technology", "gbrs_paired_asm": "GCA_004005945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/005/945/GCF_004005945.1_ASM400594v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4745991", "genome_size_ungapped": "4745991", "gc_percent": "50.000000", "replicon_count": "0", "scaffold_count": "114", "contig_count": "114", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004005945.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "4119", "protein_coding_gene_count": "4006", "non_coding_gene_count": "96", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-01-08", "dateModified": "2019-01-08", "datePublished": "2019-01-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Rheinheimera riviphila" ], "sample_taxid": [ "1834037" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Taiwan" ], "sample_host_location_id": [], "data_size": "1.344 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)": "4745991", "Number of Sequences": "114", "Longest Sequences (bp)": "569627", "N50 (bp)": "167682", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.8", "Number of CDSs": "4014", "Average Protein Length": "348.4", "Coding Ratio (%)": "88.4", "Number of rRNAs": "3", "Number of tRNAs": "82", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rheinheimera riviphila", "strain": "strain=KYPC3", "accession": "GCA_004005945.1", "taxid": 1834037, "species_taxid": 1834037, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1547, "total_fragments": 1552, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pararheinheimera texasensis", "strain": "strain=DSM 17496", "accession": "GCA_000711985.1", "taxid": 306205, "species_taxid": 306205, "relation_to_type": "type", "validated": true, "ani": 78.7307, "matched_fragments": 531, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rheinheimera tangshanensis", "strain": "strain=JA3-B52", "accession": "GCA_008017875.1", "taxid": 400153, "species_taxid": 400153, "relation_to_type": "type", "validated": true, "ani": 78.4824, "matched_fragments": 326, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rheinheimera tangshanensis", "strain": "strain=CGMCC 1.6362", "accession": "GCA_014645135.1", "taxid": 400153, "species_taxid": 400153, "relation_to_type": "type", "validated": true, "ani": 78.4134, "matched_fragments": 329, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pararheinheimera mesophila", "strain": "strain=IITR13", "accession": "GCA_003862465.1", "taxid": 1547515, "species_taxid": 1547515, "relation_to_type": "type", "validated": true, "ani": 78.3845, "matched_fragments": 339, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pararheinheimera mesophila", "strain": "strain=IITR-13", "accession": "GCA_000986865.1", "taxid": 1547515, "species_taxid": 1547515, "relation_to_type": "type", "validated": true, "ani": 78.32, "matched_fragments": 326, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rheinheimera pacifica", "strain": "strain=DSM 17616", "accession": "GCA_900108485.1", "taxid": 173990, "species_taxid": 173990, "relation_to_type": "type", "validated": true, "ani": 77.7954, "matched_fragments": 255, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rheinheimera maricola", "strain": "strain=MA-13", "accession": "GCA_016918075.2", "taxid": 2793282, "species_taxid": 2793282, "relation_to_type": "type", "validated": true, "ani": 77.6641, "matched_fragments": 200, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rheinheimera lutimaris", "strain": "strain=YQF-2", "accession": "GCA_013283795.1", "taxid": 2740584, "species_taxid": 2740584, "relation_to_type": "type", "validated": true, "ani": 77.6458, "matched_fragments": 252, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rheinheimera baltica", "strain": "strain=DSM 14885", "accession": "GCA_000425345.1", "taxid": 67576, "species_taxid": 67576, "relation_to_type": "type", "validated": true, "ani": 77.6271, "matched_fragments": 166, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alishewanella agri", "strain": "strain=BL06", "accession": "GCA_000272005.1", "taxid": 553384, "species_taxid": 553384, "relation_to_type": "type", "validated": true, "ani": 77.5853, "matched_fragments": 216, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rheinheimera hassiensis", "strain": "strain=LMG 27268", "accession": "GCA_022436675.1", "taxid": 1193627, "species_taxid": 1193627, "relation_to_type": "type", "validated": true, "ani": 77.5377, "matched_fragments": 251, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rheinheimera nanhaiensis", "strain": "strain=E407-8", "accession": "GCA_000296695.1", "taxid": 1163621, "species_taxid": 1163621, "relation_to_type": "type", "validated": true, "ani": 77.4532, "matched_fragments": 256, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004005945.1", "gtdb_species": "s__Pararheinheimera riviphila", "ani": 100.0, "matched_fragments": 1547, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera", "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_001669775.1", "gtdb_species": "s__Pararheinheimera sp001669775", "ani": 89.4784, "matched_fragments": 1322, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera", "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_018820995.1", "gtdb_species": "s__Pararheinheimera sp018820995", "ani": 81.9206, "matched_fragments": 705, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.83", "min_intra_species_ani": "98.80", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.81", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_003543135.1", "gtdb_species": "s__Pararheinheimera sp003543135", "ani": 80.3867, "matched_fragments": 668, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.83", "min_intra_species_ani": "98.83", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000711985.1", "gtdb_species": "s__Pararheinheimera texasensis", "ani": 78.7309, "matched_fragments": 530, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera", "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_008015325.1", "gtdb_species": "s__Pararheinheimera sp008015325", "ani": 78.4898, "matched_fragments": 461, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera", "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_004005375.1", "gtdb_species": "s__Pararheinheimera sp004005375", "ani": 78.2002, "matched_fragments": 311, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera", "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_018815765.1", "gtdb_species": "s__Pararheinheimera sp018815765", "ani": 77.6822, "matched_fragments": 302, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera", "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": -0.277, "cell_length": 0.194, "doubling_h": null, "growth_tmp": 29.444, "optimum_tmp": 29.75, "optimum_ph": 7.768, "genome_size": 4163180.285, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.2, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.8, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Rheinheimera", "riviphila" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }