{ "type": "genome", "identifier": "GCF_001854765.1", "organism": "Vibrio sonorensis", "title": "Vibrio sonorensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CIAD, A.C. Mazatlan Unit for Aquaculture", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001854765.1", "bioproject": "PRJNA224116", "biosample": "SAMN04029016", "wgs_master": "LJJE00000000.1", "refseq_category": "reference genome", "taxid": "1004316", "species_taxid": "1004316", "organism_name": "Vibrio sonorensis", "infraspecific_name": "strain=CAIM 1076", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/26", "asm_name": "ASM185476v1", "asm_submitter": "CIAD, A.C. Mazatlan Unit for Aquaculture", "gbrs_paired_asm": "GCA_001854765.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/854/765/GCF_001854765.1_ASM185476v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4767843", "genome_size_ungapped": "4767843", "gc_percent": "44.500000", "replicon_count": "0", "scaffold_count": "138", "contig_count": "138", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001854765.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "4722", "protein_coding_gene_count": "4123", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-26", "dateModified": "2016-10-26", "datePublished": "2016-10-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio sonorensis" ], "sample_taxid": [ "1004316" ], "sample_host_organism": [ "Crassostrea gigas (oyster)" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Mexico" ], "sample_host_location_id": [], "data_size": "1.369 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4767843", "Number of Sequences": "138", "Longest Sequences (bp)": "413688", "N50 (bp)": "189594", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.3", "Number of CDSs": "4880", "Average Protein Length": "277.4", "Coding Ratio (%)": "85.2", "Number of rRNAs": "0", "Number of tRNAs": "58", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio sonorensis", "strain": "strain=CAIM 1076", "accession": "GCA_001854765.1", "taxid": 1004316, "species_taxid": 1004316, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1536, "total_fragments": 1539, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio tubiashii", "strain": "strain=ATCC 19109", "accession": "GCA_000222665.2", "taxid": 29498, "species_taxid": 29498, "relation_to_type": "suspected-type", "validated": true, "ani": 79.7591, "matched_fragments": 359, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio tubiashii", "strain": "strain=ATCC 19109", "accession": "GCA_000772105.1", "taxid": 29498, "species_taxid": 29498, "relation_to_type": "suspected-type", "validated": true, "ani": 79.6886, "matched_fragments": 365, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio nereis", "strain": "strain=DSM 19584", "accession": "GCA_001274805.1", "taxid": 693, "species_taxid": 693, "relation_to_type": "type", "validated": true, "ani": 79.568, "matched_fragments": 348, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio nereis", "strain": "strain=NBRC 15637", "accession": "GCA_001591105.1", "taxid": 693, "species_taxid": 693, "relation_to_type": "type", "validated": true, "ani": 79.5292, "matched_fragments": 348, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio orientalis", "strain": "strain=CIP 102891", "accession": "GCA_000222645.2", "taxid": 28175, "species_taxid": 28175, "relation_to_type": "type", "validated": true, "ani": 79.4676, "matched_fragments": 367, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio orientalis", "strain": "strain=CIP 102891", "accession": "GCA_000176235.1", "taxid": 28175, "species_taxid": 28175, "relation_to_type": "type", "validated": true, "ani": 79.4633, "matched_fragments": 373, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio coralliilyticus", "strain": "strain=ATCC BAA-450", "accession": "GCA_000176135.1", "taxid": 190893, "species_taxid": 190893, "relation_to_type": "type", "validated": true, "ani": 79.4375, "matched_fragments": 359, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio bivalvicida", "strain": "strain=605", "accession": "GCA_001399455.2", "taxid": 1276888, "species_taxid": 1276888, "relation_to_type": "type", "validated": true, "ani": 79.4052, "matched_fragments": 364, "total_fragments": 1539, "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": 79.3956, "matched_fragments": 323, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio pelagius", "strain": "strain=ATCC 25916", "accession": "GCA_024347575.1", "taxid": 28169, "species_taxid": 28169, "relation_to_type": "type", "validated": true, "ani": 79.3552, "matched_fragments": 275, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio mexicanus", "strain": "strain=CAIM 1540", "accession": "GCA_001012815.1", "taxid": 1004326, "species_taxid": 1004326, "relation_to_type": "type", "validated": true, "ani": 79.3528, "matched_fragments": 335, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio rhodolitus", "strain": "strain=G98", "accession": "GCA_003350325.1", "taxid": 2231649, "species_taxid": 2231649, "relation_to_type": "type", "validated": true, "ani": 79.3524, "matched_fragments": 347, "total_fragments": 1539, "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": 79.3374, "matched_fragments": 300, "total_fragments": 1539, "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": 79.3352, "matched_fragments": 304, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio campbellii", "strain": "strain=CAIM 519", "accession": "GCA_000334195.1", "taxid": 680, "species_taxid": 680, "relation_to_type": "type", "validated": true, "ani": 79.3345, "matched_fragments": 309, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio variabilis", "strain": "strain=CAIM 1454", "accession": "GCA_003263785.1", "taxid": 990271, "species_taxid": 990271, "relation_to_type": "type", "validated": true, "ani": 79.3088, "matched_fragments": 253, "total_fragments": 1539, "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": 79.2971, "matched_fragments": 318, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio alginolyticus", "strain": "strain=NBRC 15630", "accession": "GCA_000467145.1", "taxid": 663, "species_taxid": 663, "relation_to_type": "type", "validated": true, "ani": 79.2587, "matched_fragments": 293, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio maerlii", "strain": "strain=G62", "accession": "GCA_003415655.1", "taxid": 2231648, "species_taxid": 2231648, 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio penaeicida", "strain": "strain=CAIM 285", "accession": "GCA_003970425.1", "taxid": 104609, "species_taxid": 104609, "relation_to_type": "type", "validated": true, "ani": 78.8206, "matched_fragments": 249, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio furnissii", "strain": "strain=CIP 102972", "accession": "GCA_000176175.1", "taxid": 29494, "species_taxid": 29494, "relation_to_type": "type", "validated": true, "ani": 78.5215, "matched_fragments": 260, "total_fragments": 1539, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001854765.1", "gtdb_species": "s__Vibrio sonorensis", "ani": 100.0, "matched_fragments": 1536, "total_fragments": 1539, "gtdb_taxonomy": 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