{ "type": "genome", "identifier": "GCF_004339025.1", "organism": "Volucribacter psittacicida", "title": "Volucribacter psittacicida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004339025.1", "bioproject": "PRJNA224116", "biosample": "SAMN10866318", "wgs_master": "SMFT00000000.1", "refseq_category": "reference genome", "taxid": "203482", "species_taxid": "203482", "organism_name": "Volucribacter psittacicida", "infraspecific_name": "strain=DSM 15534", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/11", "asm_name": "ASM433902v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004339025.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/339/025/GCF_004339025.1_ASM433902v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2267688", "genome_size_ungapped": "2267305", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "11", "contig_count": "11", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004339025.1-RS_2024_04_17", "annotation_date": "2024-04-17", "total_gene_count": "2177", "protein_coding_gene_count": "2084", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-11", "dateModified": "2019-03-11", "datePublished": "2019-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Volucribacter psittacicida" ], "sample_taxid": [ "203482" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "0.634 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)": "2267688", "Number of Sequences": "11", "Longest Sequences (bp)": "724385", "N50 (bp)": "712834", "Gap Ratio (%)": "0.016889", "GCcontent (%)": "38.2", "Number of CDSs": "2118", "Average Protein Length": "317.2", "Coding Ratio (%)": "88.9", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Volucribacter psittacicida", "strain": "strain=DSM 15534", "accession": "GCA_004339025.1", "taxid": 203482, "species_taxid": 203482, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 750, "total_fragments": 750, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Avibacterium avium", "strain": "strain=NCTC 11297", "accession": "GCA_900454535.1", "taxid": 751, "species_taxid": 751, "relation_to_type": "type", "validated": true, "ani": 78.027, "matched_fragments": 197, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Canicola haemoglobinophilus", "strain": "strain=CCUG 3714", "accession": "GCA_002015075.1", "taxid": 733, "species_taxid": 733, "relation_to_type": "type", "validated": true, "ani": 77.9408, "matched_fragments": 189, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Avibacterium paragallinarum", "strain": "strain=CCUG 12835", "accession": "GCA_002921155.1", "taxid": 728, "species_taxid": 728, "relation_to_type": "type", "validated": true, "ani": 77.9077, "matched_fragments": 180, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pasteurella multocida", "strain": "strain=ATCC 43137", "accession": "GCA_000754275.1", "taxid": 747, "species_taxid": 747, "relation_to_type": "type", "validated": true, "ani": 77.8933, "matched_fragments": 170, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Canicola haemoglobinophilus", "strain": "strain=NCTC1659", "accession": "GCA_900450725.1", "taxid": 733, "species_taxid": 733, "relation_to_type": "type", "validated": true, "ani": 77.889, "matched_fragments": 192, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pasteurella multocida", "strain": "strain=NCTC10322", "accession": "GCA_900187275.1", "taxid": 747, "species_taxid": 747, "relation_to_type": "type", "validated": true, "ani": 77.8593, "matched_fragments": 167, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Avibacterium paragallinarum", "strain": "strain=NCTC11296", "accession": "GCA_900450705.1", "taxid": 728, "species_taxid": 728, "relation_to_type": "type", "validated": true, "ani": 77.8096, "matched_fragments": 201, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Conservatibacter flavescens", "strain": "strain=7.4", "accession": "GCA_002795425.1", "taxid": 28161, "species_taxid": 28161, "relation_to_type": "type", "validated": true, "ani": 77.8075, "matched_fragments": 223, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pasteurella canis", "strain": "strain=NCTC11621", "accession": "GCA_900454865.1", "taxid": 753, "species_taxid": 753, "relation_to_type": "type", "validated": true, "ani": 77.7931, "matched_fragments": 160, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pasteurella multocida subsp. gallicida", "strain": "strain=NCTC10204", "accession": "GCA_900636625.1", "taxid": 123812, "species_taxid": 747, "relation_to_type": "type", "validated": true, "ani": 77.7848, "matched_fragments": 178, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cricetibacter osteomyelitidis", "strain": "strain=DSM 28404", "accession": "GCA_004340985.1", "taxid": 1521931, "species_taxid": 1521931, "relation_to_type": "type", "validated": true, "ani": 77.6835, "matched_fragments": 146, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus parainfluenzae", "strain": "strain=NCTC 7857", "accession": "GCA_900450845.1", "taxid": 729, "species_taxid": 729, "relation_to_type": "suspected-type", "validated": true, "ani": 77.6656, "matched_fragments": 148, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus seminalis", "strain": "strain=SZY H1", "accession": "GCA_006384255.1", "taxid": 2582921, "species_taxid": 2582921, "relation_to_type": "type", "validated": true, "ani": 77.6513, "matched_fragments": 128, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Basfia succiniciproducens", "strain": "strain=JF4016", "accession": "GCA_011455875.1", "taxid": 653940, "species_taxid": 653940, "relation_to_type": "suspected-type", "validated": true, "ani": 77.58, "matched_fragments": 116, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus influenzae", "strain": "strain=FDAARGOS_1560", "accession": "GCA_020736045.1", "taxid": 727, "species_taxid": 727, "relation_to_type": "type", "validated": true, "ani": 77.5343, "matched_fragments": 141, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus influenzae", "strain": "strain=NCTC8143", "accession": "GCA_001457655.1", "taxid": 727, "species_taxid": 727, "relation_to_type": "type", "validated": true, "ani": 77.4499, "matched_fragments": 145, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus haemolyticus", "strain": "strain=CCUG 12834", "accession": "GCA_001679045.1", "taxid": 726, "species_taxid": 726, "relation_to_type": "type", "validated": true, "ani": 77.3772, "matched_fragments": 135, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rodentibacter trehalosifermentans", "strain": "strain=H1987082031", "accession": "GCA_002000545.1", "taxid": 1908263, "species_taxid": 1908263, "relation_to_type": "type", "validated": true, "ani": 77.1457, "matched_fragments": 149, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aggregatibacter actinomycetemcomitans", "strain": "strain=DSM 8324", "accession": "GCA_000372365.1", "taxid": 714, "species_taxid": 714, "relation_to_type": "type", "validated": true, "ani": 77.0123, "matched_fragments": 109, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aggregatibacter actinomycetemcomitans", "strain": "strain=NCTC_9710", "accession": "GCA_008085305.1", "taxid": 714, "species_taxid": 714, "relation_to_type": "type", "validated": true, "ani": 76.8721, "matched_fragments": 106, "total_fragments": 750, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004339025.1", "gtdb_species": "s__Volucribacter psittacicida", "ani": 100.0, "matched_fragments": 750, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Volucribacter", "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_001679485.1", "gtdb_species": "s__Haemophilus_D sp001679485", "ani": 77.9653, "matched_fragments": 130, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D", "ani_circumscription_radius": 95.096, "mean_intra_species_ani": "95.82", "min_intra_species_ani": "95.82", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000210895.1", "gtdb_species": "s__Haemophilus_D parainfluenzae_A", "ani": 77.9593, "matched_fragments": 142, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.08", "min_intra_species_ani": "95.08", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { 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"GCA_905205995.1", "gtdb_species": "s__Haemophilus_D sp905205995", "ani": 77.8423, "matched_fragments": 126, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D", "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_002795425.1", "gtdb_species": "s__Conservatibacter flavescens", "ani": 77.8259, "matched_fragments": 221, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Conservatibacter", "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_900187275.1", "gtdb_species": "s__Pasteurella multocida", "ani": 77.8143, "matched_fragments": 166, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "96.53", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.57", "num_clustered_genomes": 288, "status": "-" }, { "accession": "GCF_002850605.1", "gtdb_species": "s__Pasteurella oralis", "ani": 77.7832, "matched_fragments": 173, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella", "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_900450705.1", "gtdb_species": "s__Avibacterium paragallinarum", "ani": 77.7722, "matched_fragments": 205, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.58", "min_intra_species_ani": "96.82", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.82", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_000973525.1", "gtdb_species": "s__Pasteurella multocida_A", "ani": 77.767, "matched_fragments": 157, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella", "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_900454865.1", "gtdb_species": "s__Pasteurella canis", "ani": 77.7366, 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"matched_fragments": 150, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Cricetibacter", "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": "GCA_002015125.1", "gtdb_species": "s__Pasteurella felis", "ani": 77.6212, "matched_fragments": 163, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.37", "min_intra_species_ani": "98.52", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003130075.1", "gtdb_species": "s__Aggregatibacter segnis_A", "ani": 77.6208, "matched_fragments": 122, 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750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A", "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_900475755.1", "gtdb_species": "s__Haemophilus influenzae_D", "ani": 77.4087, "matched_fragments": 140, "total_fragments": 750, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus", "ani_circumscription_radius": 95.4263, "mean_intra_species_ani": "96.90", "min_intra_species_ani": "95.46", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.81", "num_clustered_genomes": 69, "status": "-" }, { "accession": "GCF_002000125.1", "gtdb_species": "s__Rodentibacter heidelbergensis", "ani": 77.3685, "matched_fragments": 163, "total_fragments": 750, "gtdb_taxonomy": 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