{ "type": "genome", "identifier": "GCF_900460465.1", "organism": "Yersinia pestis", "title": "Yersinia pestis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900460465.1", "bioproject": "PRJNA224116", "biosample": "SAMEA104281628", "wgs_master": "UAVH00000000.1", "refseq_category": "na", "taxid": "632", "species_taxid": "632", "organism_name": "Yersinia pestis", "infraspecific_name": "strain=NCTC5923", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/29", "asm_name": "57940_B01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900460465.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/460/465/GCF_900460465.1_57940_B01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4777134", "genome_size_ungapped": "4777134", "gc_percent": "47.500000", "replicon_count": "0", "scaffold_count": "12", "contig_count": "12", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900460465.1-RS_2024_07_31", "annotation_date": "2024-07-31", "total_gene_count": "4405", "protein_coding_gene_count": "4060", "non_coding_gene_count": "100", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-29", "dateModified": "2018-06-29", "datePublished": "2018-06-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Yersinia pestis" ], "sample_taxid": [ "632" ], "sample_host_organism": [ "not available" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.354 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)": "4777134", "Number of Sequences": "12", "Longest Sequences (bp)": "1485201", "N50 (bp)": "1129548", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.6", "Number of CDSs": "4211", "Average Protein Length": "310.2", "Coding Ratio (%)": "82.0", "Number of rRNAs": "19", "Number of tRNAs": "70", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Yersinia pseudotuberculosis", "strain": "strain=NCTC10275", "accession": "GCA_900637475.1", "taxid": 633, "species_taxid": 633, "relation_to_type": "suspected-type", "validated": true, "ani": 99.1603, "matched_fragments": 1407, "total_fragments": 1586, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia similis", "strain": "strain=228", "accession": "GCA_000582515.1", "taxid": 367190, "species_taxid": 367190, "relation_to_type": "type", "validated": true, "ani": 94.7159, "matched_fragments": 1335, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia similis", "strain": "strain=Y228", "accession": "GCA_001053095.1", "taxid": 367190, "species_taxid": 367190, "relation_to_type": "type", "validated": true, "ani": 94.6773, "matched_fragments": 1310, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia intermedia", "strain": "strain=NCTC11469", "accession": "GCA_900635455.1", "taxid": 631, "species_taxid": 631, "relation_to_type": "type", "validated": true, "ani": 82.993, "matched_fragments": 883, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia intermedia", "strain": "strain=ATCC 29909", "accession": "GCA_000168035.1", 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"relation_to_type": "type", "validated": true, "ani": 82.6129, "matched_fragments": 896, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia rochesterensis", "strain": "strain=ATCC BAA-2637", "accession": "GCA_003600645.1", "taxid": 1604335, "species_taxid": 1604335, "relation_to_type": "type", "validated": true, "ani": 82.5919, "matched_fragments": 871, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia thracica", "strain": "strain=IP34646", "accession": "GCA_902170565.1", "taxid": 2890319, "species_taxid": 2890319, "relation_to_type": "type", "validated": true, "ani": 82.5534, "matched_fragments": 838, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia aldovae", "strain": "strain=IP06005", "accession": "GCA_001091225.1", "taxid": 29483, "species_taxid": 29483, "relation_to_type": "type", "validated": true, "ani": 82.3573, "matched_fragments": 861, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia nevei", "strain": "strain=S15", "accession": "GCA_008364245.1", "taxid": 2703794, "species_taxid": 2703794, "relation_to_type": "type", "validated": true, "ani": 79.0573, "matched_fragments": 331, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hafnia paralvei", "strain": "strain=ATCC 29927", "accession": "GCA_023698525.1", "taxid": 546367, "species_taxid": 546367, "relation_to_type": "type", "validated": true, "ani": 78.9784, "matched_fragments": 271, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia bockelmannii", "strain": "strain=S3", "accession": "GCA_008011855.1", "taxid": 2703793, "species_taxid": 2703793, "relation_to_type": "type", "validated": true, "ani": 78.8845, "matched_fragments": 337, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella perminowiae", "strain": "strain=SL6", "accession": "GCA_019049755.1", "taxid": 2816244, "species_taxid": 2816244, "relation_to_type": "type", "validated": true, "ani": 78.5437, "matched_fragments": 299, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900460465.1", "gtdb_species": "s__Yersinia pestis", "ani": 100.0, "matched_fragments": 1581, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.78", "min_intra_species_ani": "97.10", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.85", "num_clustered_genomes": 655, "status": "conclusive" }, { "accession": "GCF_001053095.1", "gtdb_species": 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83.0039, "matched_fragments": 884, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "97.82", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCF_001047675.1", "gtdb_species": "s__Yersinia aleksiciae", "ani": 82.8929, "matched_fragments": 821, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "98.37", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.82", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_013282745.1", "gtdb_species": "s__Yersinia bercovieri", "ani": 82.8465, 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816, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.53", "min_intra_species_ani": "99.44", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_000754805.1", "gtdb_species": "s__Yersinia frederiksenii", "ani": 82.7453, "matched_fragments": 882, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.36", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.85", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_001152565.1", "gtdb_species": "s__Yersinia pekkanenii", "ani": 82.7345, "matched_fragments": 919, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001098625.1", "gtdb_species": "s__Yersinia frederiksenii_C", "ani": 82.7109, "matched_fragments": 905, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_001123825.1", "gtdb_species": "s__Yersinia kristensenii_C", "ani": 82.6229, "matched_fragments": 845, "total_fragments": 1586, 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