{ "type": "genome", "identifier": "GCF_012275705.1", "organism": "Vibrio chemaguriensis", "title": "Vibrio chemaguriensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Indian Institute of Science Education and Research Kolkata", "publication": [ {} ], "properties": { "assembly_accession": "GCF_012275705.1", "bioproject": "PRJNA224116", "biosample": "SAMN10952912", "wgs_master": "SHOE00000000.1", "refseq_category": "reference genome", "taxid": "2527672", "species_taxid": "2527672", "organism_name": "Vibrio chemaguriensis", "infraspecific_name": "strain=Iso1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/13", "asm_name": "ASM1227570v1", "asm_submitter": "Indian Institute of Science Education and Research Kolkata", "gbrs_paired_asm": "GCA_012275705.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/012/275/705/GCF_012275705.1_ASM1227570v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5006289", "genome_size_ungapped": "5006289", "gc_percent": "45.000000", "replicon_count": "0", "scaffold_count": "67", "contig_count": "67", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_012275705.1-RS_2024_06_17", "annotation_date": "2024-06-17", "total_gene_count": "4528", "protein_coding_gene_count": "4393", "non_coding_gene_count": "86", "pubmed_id": "31280333" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-04-13", "dateModified": "2020-04-13", "datePublished": "2020-04-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio chemaguriensis" ], "sample_taxid": [ "2527672" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Sundarbans" ], "sample_host_location_id": [], "data_size": "1.433 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)": "5006289", "Number of Sequences": "67", "Longest Sequences (bp)": "523014", "N50 (bp)": "188182", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.9", "Number of CDSs": "4458", "Average Protein Length": "323.1", "Coding Ratio (%)": "86.3", "Number of rRNAs": "0", "Number of tRNAs": "79", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio antiquarius", "strain": "strain=EX25", "accession": "GCA_000024825.1", "taxid": 150340, "species_taxid": 150340, "relation_to_type": "suspected-type", "validated": true, "ani": 98.2005, "matched_fragments": 1551, "total_fragments": 1636, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio antiquarius", "strain": "strain=EX25", "accession": "GCA_000152485.1", "taxid": 150340, "species_taxid": 150340, "relation_to_type": "suspected-type", "validated": true, "ani": 98.0026, "matched_fragments": 1451, "total_fragments": 1636, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio alginolyticus", "strain": "strain=NBRC 15630", "accession": "GCA_000467145.1", "taxid": 663, "species_taxid": 663, "relation_to_type": "type", "validated": true, "ani": 92.6176, "matched_fragments": 1414, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio alginolyticus", "strain": "strain=ATCC 17749", "accession": "GCA_000354175.2", "taxid": 663, "species_taxid": 663, "relation_to_type": "type", "validated": true, "ani": 92.5789, "matched_fragments": 1451, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio alginolyticus", "strain": "strain=FDAARGOS_97", "accession": "GCA_001471275.2", "taxid": 663, "species_taxid": 663, "relation_to_type": "type", "validated": true, "ani": 92.5539, "matched_fragments": 1448, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio alginolyticus", "strain": "strain=NCTC12160", "accession": "GCA_900460285.1", "taxid": 663, "species_taxid": 663, "relation_to_type": "type", "validated": true, "ani": 92.516, "matched_fragments": 1450, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=NCTC10903", "accession": "GCA_900460535.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 87.0695, "matched_fragments": 1271, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=NBRC 12711", "accession": "GCA_000813305.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 87.0577, "matched_fragments": 1252, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=ATCC 17802", "accession": "GCA_001011015.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 86.9899, "matched_fragments": 1273, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio natriegens", "strain": "strain=14048", "accession": "GCA_024508015.1", "taxid": 691, "species_taxid": 691, "relation_to_type": "type", "validated": true, "ani": 83.0622, "matched_fragments": 902, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio panuliri", "strain": "strain=LBS 2", "accession": "GCA_008830195.1", "taxid": 1381081, "species_taxid": 1381081, "relation_to_type": "type", "validated": true, "ani": 80.1629, "matched_fragments": 390, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio panuliri", "strain": "strain=JCM 19500", "accession": "GCA_009938205.1", "taxid": 1381081, "species_taxid": 1381081, "relation_to_type": "type", "validated": true, "ani": 80.1042, "matched_fragments": 403, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio fortis", "strain": "strain=LMG 21557", "accession": "GCA_024347475.1", "taxid": 212667, "species_taxid": 212667, "relation_to_type": "type", "validated": true, "ani": 79.7702, "matched_fragments": 445, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio chagasii", "strain": "strain=LMG 21353", "accession": "GCA_024347355.1", "taxid": 170679, "species_taxid": 170679, "relation_to_type": "suspected-type", "validated": true, "ani": 79.6972, "matched_fragments": 456, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_001048675.1", "gtdb_species": "s__Vibrio diabolicus", "ani": 98.1075, "matched_fragments": 1541, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.44", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 43, "status": "conclusive" }, { "accession": "GCF_000354175.2", "gtdb_species": "s__Vibrio alginolyticus", "ani": 92.5739, "matched_fragments": 1452, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.52", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 169, "status": "-" }, { "accession": "GCF_900460535.1", "gtdb_species": "s__Vibrio parahaemolyticus", "ani": 87.0917, "matched_fragments": 1268, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "97.74", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.76", "num_clustered_genomes": 1553, "status": "-" }, { "accession": "GCF_002563795.1", "gtdb_species": "s__Vibrio sp002563795", "ani": 85.3606, "matched_fragments": 1034, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_000817815.1", "gtdb_species": "s__Vibrio owensii", "ani": 84.1013, "matched_fragments": 1023, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.72", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.79", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCF_002163755.1", "gtdb_species": "s__Vibrio campbellii", "ani": 83.8702, "matched_fragments": 982, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.60", "min_intra_species_ani": "95.95", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.77", "num_clustered_genomes": 78, "status": "-" }, { "accession": "GCF_001591145.1", "gtdb_species": "s__Vibrio harveyi", "ani": 83.7068, "matched_fragments": 1005, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.53", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_002741985.1", "gtdb_species": "s__Vibrio rotiferianus", "ani": 83.4489, "matched_fragments": 980, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.35", "min_intra_species_ani": "95.73", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_000417905.1", "gtdb_species": "s__Vibrio natriegens", "ani": 83.0933, "matched_fragments": 877, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "95.57", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCA_018222805.1", "gtdb_species": "s__Vibrio sp018222805", "ani": 82.66, "matched_fragments": 817, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_000830505.1", "gtdb_species": "s__Vibrio mytili", "ani": 82.0258, "matched_fragments": 734, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_001274785.1", "gtdb_species": "s__Vibrio hepatarius", "ani": 80.6933, "matched_fragments": 489, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "98.05", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.18, "cell_length": 0.215, "doubling_h": -0.527, "growth_tmp": 27.81, "optimum_tmp": 26.308, "optimum_ph": 7.4, "genome_size": 4870437.62, "gc_content": 44.906, "coding_genes": 4624.827, "rRNA16S_genes": 10.063, "tRNA_genes": 116.411, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.864, "range_salinity": 0.923, "facultative_respiration": 0.602, "anaerobic_respiration": 0.011, "aerobic_respiration": 0.386, "mesophilic_range_tmp": 0.976, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.023, "bacillus_cell_shape": 0.637, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.034, "vibrio_cell_shape": 0.327, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Vibrio", "chemaguriensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }