{ "type": "genome", "identifier": "GCF_002553615.1", "organism": "Clostridium neonatale", "title": "Clostridium neonatale", "description": "na", "data type": "Genome sequencing and assembly", "organization": "national microbiology laboratory", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002553615.1", "bioproject": "PRJNA224116", "biosample": "SAMN07738545", "wgs_master": "PDCJ00000000.1", "refseq_category": "na", "taxid": "137838", "species_taxid": "137838", "organism_name": "Clostridium neonatale", "infraspecific_name": "strain=LCDC 99A005", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/10/15", "asm_name": "ASM255361v1", "asm_submitter": "national microbiology laboratory", "gbrs_paired_asm": "GCA_002553615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/553/615/GCF_002553615.1_ASM255361v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4705520", "genome_size_ungapped": "4705318", "gc_percent": "28.500000", "replicon_count": "0", "scaffold_count": "7", "contig_count": "7", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002553615.1-RS_2024_03_31", "annotation_date": "2024-03-31", "total_gene_count": "4265", "protein_coding_gene_count": "4108", "non_coding_gene_count": "94", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-10-15", "dateModified": "2017-10-15", "datePublished": "2017-10-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium neonatale" ], "sample_taxid": [ "137838" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada: Winnipeg" ], "sample_host_location_id": [], "data_size": "1.273 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)": "4705520", "Number of Sequences": "7", "Longest Sequences (bp)": "3168417", "N50 (bp)": "3168417", "Gap Ratio (%)": "0.004357", "GCcontent (%)": "28.5", "Number of CDSs": "4230", "Average Protein Length": "308.0", "Coding Ratio (%)": "83.1", "Number of rRNAs": "13", "Number of tRNAs": "73", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium neonatale", "strain": "strain=LCDC 99A005", "accession": "GCA_002553615.1", "taxid": 137838, "species_taxid": 137838, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1565, "total_fragments": 1565, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium neonatale", "strain": "strain=LCDC no.99-A-005", "accession": "GCA_001458595.1", "taxid": 137838, "species_taxid": 137838, "relation_to_type": "type", "validated": true, "ani": 99.9744, "matched_fragments": 1557, "total_fragments": 1565, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium butyricum", "strain": "strain=NBRC 13949", "accession": "GCA_006742065.1", "taxid": 1492, "species_taxid": 1492, "relation_to_type": "type", "validated": true, "ani": 79.2531, "matched_fragments": 553, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium butyricum", "strain": "strain=NBRC 13949", "accession": "GCA_007992895.1", "taxid": 1492, "species_taxid": 1492, "relation_to_type": "type", "validated": true, "ani": 79.0613, "matched_fragments": 532, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium saccharobutylicum", "strain": "strain=DSM 13864", "accession": "GCA_000473995.1", "taxid": 169679, "species_taxid": 169679, "relation_to_type": "type", "validated": true, "ani": 78.9587, "matched_fragments": 499, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium butyricum", "strain": "strain=DSM 10702", "accession": "GCA_000409755.1", "taxid": 1492, "species_taxid": 1492, "relation_to_type": "type", "validated": true, "ani": 78.9455, "matched_fragments": 525, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium saccharobutylicum", "strain": "strain=DSM 13864", "accession": "GCA_001657435.1", "taxid": 169679, "species_taxid": 169679, "relation_to_type": "type", "validated": true, "ani": 78.9121, "matched_fragments": 462, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium beijerinckii", "strain": "strain=DSM 791", "accession": "GCA_018223745.1", "taxid": 1520, "species_taxid": 1520, "relation_to_type": "suspected-type", "validated": true, "ani": 78.7233, "matched_fragments": 498, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium saccharoperbutylacetonicum", "strain": "strain=N1-4(HMT)", "accession": "GCA_000340885.1", "taxid": 36745, "species_taxid": 36745, "relation_to_type": "type", "validated": true, "ani": 78.6549, "matched_fragments": 506, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium chromiireducens", "strain": "strain=DSM 23318", "accession": "GCA_002029255.1", "taxid": 225345, "species_taxid": 225345, "relation_to_type": "type", "validated": true, "ani": 78.5837, "matched_fragments": 473, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium puniceum", "strain": "strain=DSM 2619", "accession": "GCA_002006345.1", "taxid": 29367, "species_taxid": 29367, "relation_to_type": "type", "validated": true, "ani": 78.565, "matched_fragments": 534, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium beijerinckii", "strain": "strain=DSM 791", "accession": "GCA_002006445.1", "taxid": 1520, "species_taxid": 1520, "relation_to_type": "suspected-type", "validated": true, "ani": 78.5325, "matched_fragments": 486, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium cagae", "strain": "strain=Marseille-P4344", "accession": "GCA_900290265.1", "taxid": 2080751, "species_taxid": 2080751, "relation_to_type": "type", "validated": true, "ani": 78.4658, "matched_fragments": 415, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium saccharoperbutylacetonicum", "strain": "strain=ATCC 27021", "accession": "GCA_000334435.1", "taxid": 36745, "species_taxid": 36745, "relation_to_type": "type", "validated": true, "ani": 78.3679, "matched_fragments": 498, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium uliginosum", "strain": "strain=DSM 12992", "accession": "GCA_900112485.1", "taxid": 119641, "species_taxid": 119641, "relation_to_type": "type", "validated": true, "ani": 78.2393, "matched_fragments": 411, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium weizhouense", "strain": "strain=YB-6", "accession": "GCA_019431045.1", "taxid": 2859781, "species_taxid": 2859781, "relation_to_type": "type", "validated": true, "ani": 78.2067, "matched_fragments": 445, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium nigeriense", "strain": "strain=Marseille-P2414", "accession": "GCA_900086595.1", "taxid": 1805470, "species_taxid": 1805470, "relation_to_type": "type", "validated": true, "ani": 77.3267, "matched_fragments": 279, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium gallinarum", "strain": "strain=Sa3CUN1", "accession": "GCA_014836325.1", "taxid": 2762246, "species_taxid": 2762246, "relation_to_type": "type", "validated": true, "ani": 77.2697, "matched_fragments": 286, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidibacter thalassicus", "strain": "strain=DSM 15285", "accession": "GCA_900129915.1", "taxid": 214905, "species_taxid": 214905, "relation_to_type": "type", "validated": true, "ani": 75.3328, "matched_fragments": 88, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Abyssisolibacter fermentans", "strain": "strain=MCWD3", "accession": "GCA_001559865.1", "taxid": 1766203, "species_taxid": 1766203, "relation_to_type": "type", "validated": true, "ani": 74.8767, "matched_fragments": 104, "total_fragments": 1565, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001458595.1", "gtdb_species": "s__Clostridium neonatale", "ani": 99.9744, "matched_fragments": 1557, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.80", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCA_015058475.1", "gtdb_species": "s__Clostridium butyricum_B", "ani": 84.8693, "matched_fragments": 717, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_006742065.1", "gtdb_species": "s__Clostridium butyricum", "ani": 79.2602, "matched_fragments": 554, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "97.46", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.80", "num_clustered_genomes": 64, "status": "-" }, { "accession": "GCA_003129525.1", "gtdb_species": "s__Clostridium beijerinckii_D", "ani": 79.1339, "matched_fragments": 458, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_015058525.1", "gtdb_species": "s__Clostridium butyricum_A", "ani": 79.1094, "matched_fragments": 309, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_000473995.1", "gtdb_species": "s__Clostridium saccharobutylicum", "ani": 79.023, "matched_fragments": 496, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "95.82", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.83", "num_clustered_genomes": 65, "status": "-" }, { "accession": "GCF_012843905.1", "gtdb_species": "s__Clostridium sp012843905", "ani": 78.9099, "matched_fragments": 417, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_018223745.1", "gtdb_species": "s__Clostridium beijerinckii", "ani": 78.7295, "matched_fragments": 498, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.01", "min_intra_species_ani": "95.18", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.79", "num_clustered_genomes": 244, "status": "-" }, { "accession": "GCF_000340885.1", "gtdb_species": "s__Clostridium saccharoperbutylacetonicum", "ani": 78.6101, "matched_fragments": 506, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002029255.1", "gtdb_species": "s__Clostridium chromiireducens", "ani": 78.5461, "matched_fragments": 478, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "97.40", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002006345.1", "gtdb_species": "s__Clostridium puniceum", "ani": 78.5271, "matched_fragments": 539, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_003539755.1", "gtdb_species": "s__Clostridium sp003539755", "ani": 78.4716, "matched_fragments": 317, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_000230835.1", "gtdb_species": "s__Clostridium sp000230835", "ani": 78.4301, "matched_fragments": 479, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.12", "min_intra_species_ani": "96.12", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009928485.1", "gtdb_species": "s__Clostridium sp009928485", "ani": 78.3778, "matched_fragments": 509, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_002760435.1", "gtdb_species": "s__Clostridium sp002760435", "ani": 78.3369, "matched_fragments": 467, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900112485.1", "gtdb_species": "s__Clostridium uliginosum", "ani": 78.2227, "matched_fragments": 411, "total_fragments": 1565, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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": -0.16, "cell_length": 0.434, "doubling_h": 0.353, "growth_tmp": 37.0, "optimum_tmp": 35.173, "optimum_ph": 6.947, "genome_size": 4710840.0, "gc_content": 29.49, "coding_genes": 3796.985, "rRNA16S_genes": 9.374, "tRNA_genes": 78.312, "gram_stain": 0.945, "sporulation": 0.967, "motility": 0.92, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.944, "thermophilic_range_tmp": 0.055, "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": [ "Clostridium", "neonatale" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }