{ "type": "genome", "identifier": "GCF_023349145.1", "organism": "Shewanella fodinae", "title": "Shewanella fodinae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Karolinska Institutet", "publication": [ {} ], "properties": { "assembly_accession": "GCF_023349145.1", "bioproject": "PRJNA224116", "biosample": "SAMN24537890", "wgs_master": "JAKILP000000000.1", "refseq_category": "reference genome", "taxid": "552357", "species_taxid": "552357", "organism_name": "Shewanella fodinae", "infraspecific_name": "strain=CCUG 57102", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/05/12", "asm_name": "ASM2334914v1", "asm_submitter": "Karolinska Institutet", "gbrs_paired_asm": "GCA_023349145.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/023/349/145/GCF_023349145.1_ASM2334914v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3903445", "genome_size_ungapped": "3903445", "gc_percent": "48.500000", "replicon_count": "0", "scaffold_count": "54", "contig_count": "54", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_023349145.1-RS_2024_05_19", "annotation_date": "2024-05-19", "total_gene_count": "3623", "protein_coding_gene_count": "3487", "non_coding_gene_count": "101", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-05-12", "dateModified": "2022-05-12", "datePublished": "2022-05-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella fodinae" ], "sample_taxid": [ "552357" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Godavarikhani" ], "sample_host_location_id": [], "data_size": "1.118 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)": "3903445", "Number of Sequences": "54", "Longest Sequences (bp)": "443164", "N50 (bp)": "134899", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "48.6", "Number of CDSs": "3508", "Average Protein Length": "325.7", "Coding Ratio (%)": "87.8", "Number of rRNAs": "2", "Number of tRNAs": "82", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella fodinae", "strain": "strain=CCUG 57102", "accession": "GCA_023349145.1", "taxid": 552357, "species_taxid": 552357, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1271, "total_fragments": 1276, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella fodinae", "strain": "strain=KCTC 22506", "accession": "GCA_014651955.1", "taxid": 552357, "species_taxid": 552357, "relation_to_type": "type", "validated": true, "ani": 99.9975, "matched_fragments": 1270, "total_fragments": 1276, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella dokdonensis", "strain": "strain=DSM 23626", "accession": "GCA_018394335.1", "taxid": 712036, "species_taxid": 712036, "relation_to_type": "type", "validated": true, "ani": 85.6424, "matched_fragments": 1057, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella yunxiaonensis", "strain": "strain=FJAT-54481", "accession": "GCA_018223345.1", "taxid": 2829809, "species_taxid": 2829809, "relation_to_type": "type", "validated": true, "ani": 81.3188, "matched_fragments": 727, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=KCTC 22540", "accession": "GCA_014651975.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 78.1457, "matched_fragments": 231, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=JC5", "accession": "GCA_003217175.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 78.1099, "matched_fragments": 236, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella avicenniae", "strain": "strain=FJAT-51800", "accession": "GCA_017354945.1", "taxid": 2814294, "species_taxid": 2814294, "relation_to_type": "type", "validated": true, "ani": 78.0191, "matched_fragments": 295, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella oneidensis", "strain": "strain=MR-1", "accession": "GCA_013267215.1", "taxid": 70863, "species_taxid": 70863, "relation_to_type": "type", "validated": true, "ani": 77.8758, "matched_fragments": 157, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella sedimentimangrovi", "strain": "strain=FJAT-52962", "accession": "GCA_017354965.1", "taxid": 2814293, "species_taxid": 2814293, "relation_to_type": "type", "validated": true, "ani": 77.7785, "matched_fragments": 165, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella violacea", "strain": "strain=DSS12", "accession": "GCA_000091325.1", "taxid": 60217, "species_taxid": 60217, "relation_to_type": "type", "validated": true, "ani": 77.4724, "matched_fragments": 83, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella canadensis", "strain": "strain=HAW-EB2", "accession": "GCA_003966225.1", "taxid": 271096, "species_taxid": 271096, "relation_to_type": "type", "validated": true, "ani": 77.181, "matched_fragments": 96, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014651955.1", "gtdb_species": "s__Shewanella fodinae", "ani": 99.9975, "matched_fragments": 1270, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.57", "min_intra_species_ani": "97.13", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_018394335.1", "gtdb_species": "s__Shewanella dokdonensis", "ani": 85.6213, "matched_fragments": 1059, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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_018223345.1", "gtdb_species": "s__Shewanella sp018223345", "ani": 81.3077, "matched_fragments": 729, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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_000753795.1", "gtdb_species": "s__Shewanella mangrovi", "ani": 78.2351, "matched_fragments": 297, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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_000015245.1", "gtdb_species": "s__Shewanella amazonensis", "ani": 78.1682, "matched_fragments": 158, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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_014647855.1", "gtdb_species": "s__Shewanella gelidii", "ani": 78.0751, "matched_fragments": 74, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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_017354985.1", "gtdb_species": "s__Shewanella sp017354985", "ani": 78.0431, "matched_fragments": 162, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.75", "min_intra_species_ani": "95.81", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_017354945.1", "gtdb_species": "s__Shewanella sp017354945", "ani": 78.0091, "matched_fragments": 298, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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_002836945.1", "gtdb_species": "s__Shewanella chilikensis", "ani": 77.9736, "matched_fragments": 226, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.7827, "mean_intra_species_ani": "99.40", "min_intra_species_ani": "98.79", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000146165.2", "gtdb_species": "s__Shewanella oneidensis", "ani": 77.8881, "matched_fragments": 161, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016406305.1", "gtdb_species": "s__Shewanella putrefaciens_C", "ani": 77.783, "matched_fragments": 164, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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_002215585.1", "gtdb_species": "s__Shewanella marisflavi", "ani": 77.5315, "matched_fragments": 123, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.20", "min_intra_species_ani": "98.16", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000518705.1", "gtdb_species": "s__Shewanella colwelliana", "ani": 77.3825, "matched_fragments": 97, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003966225.1", "gtdb_species": "s__Shewanella canadensis", "ani": 77.1824, "matched_fragments": 95, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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": -0.205, "cell_length": 0.352, "doubling_h": 0.077, "growth_tmp": 22.402, "optimum_tmp": 33.5, "optimum_ph": 6.0, "genome_size": 4868941.65, "gc_content": 46.142, "coding_genes": 4161.776, "rRNA16S_genes": 9.437, "tRNA_genes": 107.731, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.333, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.812, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.187, "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": [ "Shewanella", "fodinae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }