{ "type": "genome", "identifier": "GCF_900445635.1", "organism": "Bartonella grahamii", "title": "Bartonella grahamii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900445635.1", "bioproject": "PRJNA224116", "biosample": "SAMEA44539168", "wgs_master": "UFTD00000000.1", "refseq_category": "na", "taxid": "33045", "species_taxid": "33045", "organism_name": "Bartonella grahamii", "infraspecific_name": "strain=NCTC12860", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/25", "asm_name": "51184_C02", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900445635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/445/635/GCF_900445635.1_51184_C02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2385853", "genome_size_ungapped": "2385853", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900445635.1-RS_2024_04_25", "annotation_date": "2024-04-25", "total_gene_count": "2092", "protein_coding_gene_count": "1951", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-25", "dateModified": "2018-07-25", "datePublished": "2018-07-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Bartonella grahamii" ], "sample_taxid": [ "33045" ], "sample_host_organism": [ "Bank Vole" ], "sample_host_organism_id": [], "sample_host_disease": [ "disease" ], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "0.662 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)": "2385853", "Number of Sequences": "5", "Longest Sequences (bp)": "1314855", "N50 (bp)": "1314855", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.2", "Number of CDSs": "2073", "Average Protein Length": "290.3", "Coding Ratio (%)": "75.7", "Number of rRNAs": "6", "Number of tRNAs": "42", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bartonella grahamii", "strain": "strain=NCTC12860", "accession": "GCA_900445635.1", "taxid": 33045, "species_taxid": 33045, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 788, "total_fragments": 793, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bartonella grahamii", "strain": "strain=ATCC 700132", "accession": "GCA_000518085.1", "taxid": 33045, "species_taxid": 33045, "relation_to_type": "type", "validated": true, "ani": 99.9242, "matched_fragments": 695, "total_fragments": 793, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bartonella tribocorum", "strain": "strain=type strain:506 = CIP 105476", "accession": "GCA_000196435.1", "taxid": 85701, "species_taxid": 85701, "relation_to_type": "suspected-type", "validated": true, "ani": 88.7595, "matched_fragments": 675, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella gabonensis", "strain": "strain=669", "accession": "GCA_903679515.1", "taxid": 2699889, "species_taxid": 2699889, "relation_to_type": "type", "validated": true, "ani": 88.5242, "matched_fragments": 559, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella kosoyi", "strain": "strain=Tel Aviv", "accession": "GCA_003606325.3", "taxid": 2133959, "species_taxid": 2133959, "relation_to_type": "type", "validated": true, "ani": 88.4224, "matched_fragments": 647, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella elizabethae", "strain": "strain=ATCC 49927", "accession": "GCA_000518165.1", "taxid": 807, "species_taxid": 807, "relation_to_type": "type", "validated": true, "ani": 88.3241, "matched_fragments": 577, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella mastomydis", "strain": "strain=008", "accession": "GCA_900185775.1", "taxid": 1820002, "species_taxid": 1820002, "relation_to_type": "type", "validated": true, "ani": 88.2246, "matched_fragments": 604, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella elizabethae", "strain": "strain=F9251", "accession": "GCA_000278315.1", "taxid": 807, "species_taxid": 807, "relation_to_type": "type", "validated": true, "ani": 88.1511, "matched_fragments": 592, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella rattimassiliensis", "strain": "strain=15908", "accession": "GCA_000312605.2", "taxid": 270250, "species_taxid": 270250, "relation_to_type": "type", "validated": true, "ani": 88.0876, "matched_fragments": 552, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella fuyuanensis", "strain": "strain=DSM 100694", "accession": "GCA_014197255.1", "taxid": 1460968, "species_taxid": 1460968, "relation_to_type": "type", "validated": true, "ani": 87.8255, "matched_fragments": 561, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella rattimassiliensis", "strain": "strain=15908", "accession": "GCA_000278215.1", "taxid": 270250, "species_taxid": 270250, "relation_to_type": "type", "validated": true, "ani": 87.7226, "matched_fragments": 598, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella krasnovii", "strain": "strain=OE 1-1", "accession": "GCA_003606345.3", "taxid": 2267275, "species_taxid": 2267275, "relation_to_type": "type", "validated": true, "ani": 87.7201, "matched_fragments": 632, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella saheliensis", "strain": "strain=077", "accession": "GCA_902162175.1", "taxid": 1457016, "species_taxid": 1457016, "relation_to_type": "type", "validated": true, "ani": 87.0632, "matched_fragments": 526, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella doshiae", "strain": "strain=NCTC 12862", "accession": "GCA_000278155.1", "taxid": 33044, "species_taxid": 33044, "relation_to_type": "type", "validated": true, "ani": 83.6042, "matched_fragments": 496, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella vinsonii subsp. berkhoffii", "strain": "strain=CIP 104960", "accession": "GCA_902825225.1", "taxid": 40933, "species_taxid": 33047, "relation_to_type": "type", "validated": true, "ani": 83.5848, "matched_fragments": 514, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella florencae", "strain": "strain=R4", "accession": "GCA_000312525.1", "taxid": 928210, "species_taxid": 928210, "relation_to_type": "type", "validated": true, "ani": 83.5427, "matched_fragments": 551, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella vinsonii subsp. arupensis", "strain": "strain=ATCC 700727", "accession": "GCA_902825115.1", "taxid": 110578, "species_taxid": 33047, "relation_to_type": "type", "validated": true, "ani": 83.5418, "matched_fragments": 495, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella doshiae", "strain": "strain=NCTC12862", "accession": "GCA_900445535.1", "taxid": 33044, "species_taxid": 33044, "relation_to_type": "type", "validated": true, "ani": 83.5118, "matched_fragments": 501, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella vinsonii subsp. arupensis", "strain": "strain=OK-94-513", "accession": "GCA_000278235.1", "taxid": 110578, "species_taxid": 33047, "relation_to_type": "type", "validated": true, "ani": 83.4705, "matched_fragments": 514, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella callosciuri", "strain": "strain=DSM 28538", "accession": "GCA_014203215.1", "taxid": 686223, "species_taxid": 686223, "relation_to_type": "type", "validated": true, "ani": 83.2333, "matched_fragments": 483, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella henselae", "strain": "strain=Houston-I", "accession": "GCA_002735245.1", "taxid": 38323, "species_taxid": 38323, "relation_to_type": "type", "validated": true, "ani": 83.091, "matched_fragments": 516, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella henselae", "strain": "strain=FDAARGOS_1462", "accession": "GCA_019930925.1", "taxid": 38323, "species_taxid": 38323, "relation_to_type": "type", "validated": true, "ani": 83.0058, "matched_fragments": 512, "total_fragments": 793, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000518085.1", "gtdb_species": "s__Bartonella grahamii", "ani": 99.9052, "matched_fragments": 696, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.67", "min_intra_species_ani": "99.54", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_000196435.1", "gtdb_species": "s__Bartonella tribocorum", "ani": 88.7776, "matched_fragments": 670, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018155095.1", "gtdb_species": "s__Bartonella queenslandensis_B", "ani": 88.6136, "matched_fragments": 586, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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_903679515.1", "gtdb_species": "s__Bartonella gabonensis", "ani": 88.5224, "matched_fragments": 559, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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_002777915.1", "gtdb_species": "s__Bartonella tribocorum_A", "ani": 88.505, "matched_fragments": 622, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003606325.2", "gtdb_species": "s__Bartonella kosoyi", "ani": 88.417, "matched_fragments": 641, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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_002778015.1", "gtdb_species": "s__Bartonella tribocorum_B", "ani": 88.3879, "matched_fragments": 578, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000518165.1", "gtdb_species": "s__Bartonella elizabethae", "ani": 88.3249, "matched_fragments": 577, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "95.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000312585.1", "gtdb_species": "s__Bartonella queenslandensis_A", "ani": 88.1229, "matched_fragments": 601, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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_014197255.1", "gtdb_species": "s__Bartonella fuyuanensis", "ani": 87.8593, "matched_fragments": 559, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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_000278215.1", "gtdb_species": "s__Bartonella rattimassiliensis", "ani": 87.7558, "matched_fragments": 596, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003606345.3", "gtdb_species": "s__Bartonella krasnovii", "ani": 87.7062, "matched_fragments": 634, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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_902150025.1", "gtdb_species": "s__Bartonella massiliensis", "ani": 87.5715, "matched_fragments": 620, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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_000278295.1", "gtdb_species": "s__Bartonella taylorii", "ani": 84.348, "matched_fragments": 548, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "97.76", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_902825235.1", "gtdb_species": "s__Bartonella vinsonii", "ani": 84.2009, "matched_fragments": 534, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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_000278155.1", "gtdb_species": "s__Bartonella doshiae", "ani": 83.6017, "matched_fragments": 496, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.97", "min_intra_species_ani": "97.90", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.87", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000312525.1", "gtdb_species": "s__Bartonella florencae", "ani": 83.5512, "matched_fragments": 550, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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_000278235.1", "gtdb_species": "s__Bartonella arupensis", "ani": 83.4636, "matched_fragments": 515, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.53", "min_intra_species_ani": "99.17", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000278135.1", "gtdb_species": "s__Bartonella washoeensis", "ani": 83.2691, "matched_fragments": 524, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.94", "min_intra_species_ani": "98.02", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000312545.1", "gtdb_species": "s__Bartonella senegalensis", "ani": 82.5699, "matched_fragments": 524, "total_fragments": 793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella", "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": -0.315, "cell_length": 0.071, "doubling_h": 0.627, "growth_tmp": 37.0, "optimum_tmp": 36.0, "optimum_ph": 7.3, "genome_size": 2319878.0, "gc_content": 37.615, "coding_genes": 1835.667, "rRNA16S_genes": 2.0, "tRNA_genes": 42.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Bartonella", "grahamii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }