{ "type": "genome", "identifier": "GCF_023283475.1", "organism": "Shewanella chilikensis", "title": "Shewanella chilikensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Karolinska Institutet", "publication": [ {} ], "properties": { "assembly_accession": "GCF_023283475.1", "bioproject": "PRJNA224116", "biosample": "SAMN24537896", "wgs_master": "JAKILV000000000.1", "refseq_category": "na", "taxid": "558541", "species_taxid": "558541", "organism_name": "Shewanella chilikensis", "infraspecific_name": "strain=CCUG 57101", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/05/09", "asm_name": "ASM2328347v1", "asm_submitter": "Karolinska Institutet", "gbrs_paired_asm": "GCA_023283475.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/023/283/475/GCF_023283475.1_ASM2328347v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4454714", "genome_size_ungapped": "4454714", "gc_percent": "52.500000", "replicon_count": "0", "scaffold_count": "82", "contig_count": "82", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_023283475.1-RS_2024_05_18", "annotation_date": "2024-05-18", "total_gene_count": "4034", "protein_coding_gene_count": "3869", "non_coding_gene_count": "109", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-05-09", "dateModified": "2022-05-09", "datePublished": "2022-05-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella chilikensis" ], "sample_taxid": [ "558541" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Chilika Lagoon" ], "sample_host_location_id": [], "data_size": "1.269 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)": "4454714", "Number of Sequences": "82", "Longest Sequences (bp)": "309364", "N50 (bp)": "120353", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.4", "Number of CDSs": "3942", "Average Protein Length": "326.7", "Coding Ratio (%)": "86.7", "Number of rRNAs": "4", "Number of tRNAs": "90", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella chilikensis", "strain": "strain=CCUG 57101", "accession": "GCA_023283475.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1447, "total_fragments": 1452, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=JC5", "accession": "GCA_003217175.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 99.9892, "matched_fragments": 1422, "total_fragments": 1452, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=KCTC 22540", "accession": "GCA_014651975.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 99.9781, "matched_fragments": 1405, "total_fragments": 1452, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=JC5", "accession": "GCA_002836945.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 99.9631, "matched_fragments": 1388, "total_fragments": 1452, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Shewanella indica", "strain": "strain=KJW27", "accession": "GCA_002836975.1", "taxid": 768528, "species_taxid": 768528, "relation_to_type": "type", "validated": true, "ani": 95.7278, "matched_fragments": 1336, "total_fragments": 1452, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Shewanella algae", "strain": "strain=NBRC 103173", "accession": "GCA_001598875.1", "taxid": 38313, "species_taxid": 38313, "relation_to_type": "type", "validated": true, "ani": 94.5021, "matched_fragments": 1261, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella carassii", "strain": "strain=08MAS2251", "accession": "GCA_002777975.1", "taxid": 1987584, "species_taxid": 1987584, "relation_to_type": "type", "validated": true, "ani": 93.509, "matched_fragments": 1244, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella jiangmenensis", "strain": "strain=JM162201", "accession": "GCA_018596335.1", 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"relation_to_type": "type", "validated": true, "ani": 77.9193, "matched_fragments": 338, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002836945.1", "gtdb_species": "s__Shewanella chilikensis", "ani": 99.9631, "matched_fragments": 1388, "total_fragments": 1452, "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": "conclusive" }, { "accession": "GCF_002836975.1", "gtdb_species": "s__Shewanella indica", "ani": 95.7278, "matched_fragments": 1336, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.7827, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "98.01", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_009183365.2", "gtdb_species": "s__Shewanella algae", "ani": 94.4602, "matched_fragments": 1335, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.21", "min_intra_species_ani": "97.66", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 87, "status": "-" }, { "accession": "GCF_002777975.1", "gtdb_species": "s__Shewanella carassii", "ani": 93.509, "matched_fragments": 1244, "total_fragments": 1452, "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_017354985.1", "gtdb_species": "s__Shewanella sp017354985", "ani": 78.9259, "matched_fragments": 450, "total_fragments": 1452, "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_003957745.1", "gtdb_species": "s__Shewanella khirikhana", "ani": 78.509, "matched_fragments": 473, "total_fragments": 1452, "gtdb_taxonomy": 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"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_018394335.1", "gtdb_species": "s__Shewanella dokdonensis", "ani": 78.1316, "matched_fragments": 241, "total_fragments": 1452, "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": -0.125, "cell_length": 0.243, "doubling_h": 0.077, "growth_tmp": 22.402, "optimum_tmp": 29.0, "optimum_ph": 8.0, "genome_size": 4441258.0, 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