{ "type": "genome", "identifier": "GCF_000312545.1", "organism": "Bartonella senegalensis OS02", "title": "Bartonella senegalensis OS02", "description": "na", "data type": "Genome sequencing and assembly", "organization": "ebi", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000312545.1", "bioproject": "PRJNA224116", "biosample": "SAMEA2272101", "wgs_master": "CALV00000000.1", "refseq_category": "reference genome", "taxid": "929794", "species_taxid": "1468418", "organism_name": "Bartonella senegalensis OS02", "infraspecific_name": "strain=OS02", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/10/03", "asm_name": "ASM31254v1", "asm_submitter": "ebi", "gbrs_paired_asm": "GCA_000312545.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/312/545/GCF_000312545.1_ASM31254v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2002317", "genome_size_ungapped": "1956883", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "41", "contig_count": "99", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2023-04-24", "total_gene_count": "1668", "protein_coding_gene_count": "1480", "non_coding_gene_count": "46", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-10-03", "dateModified": "2012-10-03", "datePublished": "2012-10-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Bartonella senegalensis OS02" ], "sample_taxid": [ "929794" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.553 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)": "2002317", "Number of Sequences": "41", "Longest Sequences (bp)": "1115077", "N50 (bp)": "1115077", "Gap Ratio (%)": "2.269321", "GCcontent (%)": "38.6", "Number of CDSs": "1592", "Average Protein Length": "289.9", "Coding Ratio (%)": "69.1", "Number of rRNAs": "3", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bartonella senegalensis", "strain": "strain=OS02", "accession": "GCA_000312545.1", "taxid": 1468418, "species_taxid": 1468418, "relation_to_type": "type", "validated": true, "ani": 99.9997, "matched_fragments": 649, "total_fragments": 655, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bartonella henselae", "strain": "strain=Houston-1", "accession": "GCA_000046705.1", "taxid": 38323, "species_taxid": 38323, "relation_to_type": "type", "validated": true, "ani": 89.4521, "matched_fragments": 554, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella henselae", "strain": "strain=FDAARGOS_175", "accession": "GCA_001525625.2", "taxid": 38323, "species_taxid": 38323, "relation_to_type": "type", "validated": true, "ani": 89.3544, "matched_fragments": 562, "total_fragments": 655, "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": 89.351, "matched_fragments": 561, "total_fragments": 655, "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": 89.3426, "matched_fragments": 562, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella henselae", "strain": "strain=G-5436", "accession": "GCA_021560445.1", "taxid": 38323, "species_taxid": 38323, "relation_to_type": "type", "validated": true, "ani": 89.3343, "matched_fragments": 555, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella koehlerae subsp. koehlerae", "strain": "strain=C-29", "accession": "GCA_000706625.1", "taxid": 1819240, "species_taxid": 92181, "relation_to_type": "type", "validated": true, "ani": 88.8776, "matched_fragments": 530, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella alsatica", "strain": "strain=IBS 382", "accession": "GCA_000280015.1", "taxid": 52764, "species_taxid": 52764, "relation_to_type": "type", "validated": true, "ani": 83.6178, "matched_fragments": 459, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella alsatica", "strain": "strain=CIP 105477", "accession": "GCA_013388295.1", "taxid": 52764, "species_taxid": 52764, "relation_to_type": "type", "validated": true, "ani": 83.4714, "matched_fragments": 466, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella phoceensis", "strain": "strain=CIP107707", "accession": "GCA_902825145.1", "taxid": 270249, "species_taxid": 270249, "relation_to_type": "type", "validated": true, "ani": 83.4452, "matched_fragments": 477, "total_fragments": 655, "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": 83.4274, "matched_fragments": 481, "total_fragments": 655, "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": 83.3694, "matched_fragments": 476, "total_fragments": 655, "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": 82.6079, "matched_fragments": 430, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bartonella harrusi", "strain": "strain=117A", "accession": "GCA_024297065.1", "taxid": 2961895, "species_taxid": 2961895, "relation_to_type": "type", "validated": true, "ani": 82.1706, "matched_fragments": 506, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000312545.1", "gtdb_species": "s__Bartonella senegalensis", "ani": 99.9997, "matched_fragments": 649, "total_fragments": 655, "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": "conclusive" }, { "accession": "GCF_000046705.1", "gtdb_species": "s__Bartonella henselae", "ani": 89.4521, "matched_fragments": 554, "total_fragments": 655, "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": "99.52", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.94", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCF_000706625.1", "gtdb_species": "s__Bartonella koehlerae", "ani": 88.8776, "matched_fragments": 530, "total_fragments": 655, "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": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009936175.1", "gtdb_species": "s__Bartonella quintana", "ani": 85.3146, "matched_fragments": 466, "total_fragments": 655, "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": "98.46", "min_intra_species_ani": "98.37", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.97", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_000278135.1", "gtdb_species": "s__Bartonella washoeensis", "ani": 83.9621, "matched_fragments": 497, "total_fragments": 655, "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_000278295.1", "gtdb_species": "s__Bartonella taylorii", "ani": 83.8583, "matched_fragments": 525, "total_fragments": 655, "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_000312525.1", "gtdb_species": "s__Bartonella florencae", "ani": 83.7996, "matched_fragments": 510, "total_fragments": 655, "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_013388295.1", "gtdb_species": "s__Bartonella alsatica", "ani": 83.4714, "matched_fragments": 466, "total_fragments": 655, "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": "99.98", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_902825145.1", "gtdb_species": "s__Bartonella phoceensis", "ani": 83.4452, "matched_fragments": 477, "total_fragments": 655, "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_902825235.1", "gtdb_species": "s__Bartonella vinsonii", "ani": 83.4206, "matched_fragments": 500, "total_fragments": 655, "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_000273375.1", "gtdb_species": "s__Bartonella birtlesii", "ani": 83.364, "matched_fragments": 496, "total_fragments": 655, "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": "99.71", "min_intra_species_ani": "99.25", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002777915.1", "gtdb_species": "s__Bartonella tribocorum_A", "ani": 82.3644, "matched_fragments": 503, "total_fragments": 655, "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": 82.1276, "matched_fragments": 484, "total_fragments": 655, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.315, "cell_length": 0.071, "doubling_h": 0.627, "growth_tmp": 36.224, "optimum_tmp": 33.909, "optimum_ph": 7.366, "genome_size": 1912158.156, "gc_content": 38.327, "coding_genes": 1584.487, "rRNA16S_genes": 2.0, "tRNA_genes": 42.703, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.583, "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": 0.687, "coccus_cell_shape": 0.062, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.25, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Bartonella", "senegalensis", "OS02" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }