{ "type": "genome", "identifier": "GCF_019977655.1", "organism": "Clostridium gelidum", "title": "Clostridium gelidum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Hirosaki University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019977655.1", "bioproject": "PRJNA224116", "biosample": "SAMD00388684", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "704125", "species_taxid": "704125", "organism_name": "Clostridium gelidum", "infraspecific_name": "strain=C5S11", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/31", "asm_name": "ASM1997765v1", "asm_submitter": "Hirosaki University", "gbrs_paired_asm": "GCA_019977655.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/977/655/GCF_019977655.1_ASM1997765v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6041432", "genome_size_ungapped": "6041432", "gc_percent": "29.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019977655.1-RS_2024_11_20", "annotation_date": "2024-11-20", "total_gene_count": "5592", "protein_coding_gene_count": "5385", "non_coding_gene_count": "115", "pubmed_id": "35998019" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-07-31", "dateModified": "2021-07-31", "datePublished": "2021-07-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium gelidum" ], "sample_taxid": [ "704125" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Tsuruoka-shi, Fujishima" ], "sample_host_location_id": [], "data_size": "1.636 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)": "6041432", "Number of Sequences": "1", "Longest Sequences (bp)": "6041432", "N50 (bp)": "6041432", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "29.0", "Number of CDSs": "5544", "Average Protein Length": "298.6", "Coding Ratio (%)": "82.2", "Number of rRNAs": "31", "Number of tRNAs": "79", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium gelidum", "strain": "strain=C5S11", "accession": "GCA_019977655.1", "taxid": 704125, "species_taxid": 704125, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2012, "total_fragments": 2013, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium puniceum", "strain": "strain=DSM 2619", "accession": "GCA_002006345.1", "taxid": 29367, "species_taxid": 29367, "relation_to_type": "type", "validated": true, "ani": 83.6434, "matched_fragments": 1010, "total_fragments": 2013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium diolis", "strain": "strain=DSM 15410", "accession": "GCA_008705175.1", "taxid": 223919, "species_taxid": 223919, "relation_to_type": "suspected-type", "validated": true, "ani": 81.2866, "matched_fragments": 924, "total_fragments": 2013, "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": 81.2578, "matched_fragments": 951, "total_fragments": 2013, "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": 81.1182, "matched_fragments": 881, "total_fragments": 2013, "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": 81.0704, "matched_fragments": 869, "total_fragments": 2013, "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": 80.9186, "matched_fragments": 957, "total_fragments": 2013, "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": 80.8544, "matched_fragments": 783, "total_fragments": 2013, "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": 80.7201, "matched_fragments": 933, "total_fragments": 2013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium cibarium", "strain": "strain=Sa3CVN1", "accession": "GCA_014836335.1", "taxid": 2762247, "species_taxid": 2762247, "relation_to_type": "type", "validated": true, "ani": 77.5859, "matched_fragments": 350, "total_fragments": 2013, "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": 77.4956, "matched_fragments": 261, "total_fragments": 2013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium moniliforme", "strain": "strain=DSM 3984", "accession": "GCA_017873235.1", "taxid": 39489, "species_taxid": 39489, "relation_to_type": "type", "validated": true, "ani": 77.1833, "matched_fragments": 250, "total_fragments": 2013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium sardiniense", "strain": "strain=DSM 2632", "accession": "GCA_016907995.1", "taxid": 29369, "species_taxid": 29369, "relation_to_type": "type", "validated": true, "ani": 77.0637, "matched_fragments": 270, "total_fragments": 2013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium mediterraneense", "strain": "strain=Marseille-P2434", "accession": "GCA_900091705.1", "taxid": 1805472, "species_taxid": 1805472, "relation_to_type": "type", "validated": true, "ani": 77.0325, "matched_fragments": 197, "total_fragments": 2013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium muellerianum", "strain": "strain=P21", "accession": "GCA_012926525.1", "taxid": 2716538, "species_taxid": 2716538, "relation_to_type": "type", "validated": true, "ani": 76.7651, "matched_fragments": 258, "total_fragments": 2013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium tertium", "strain": "strain=DSM 2485", "accession": "GCA_017873245.1", "taxid": 1559, "species_taxid": 1559, "relation_to_type": "type", "validated": true, "ani": 76.7625, "matched_fragments": 270, "total_fragments": 2013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hathewaya massiliensis", "strain": "strain=Marseille-P3545", "accession": "GCA_902143515.1", "taxid": 1964382, "species_taxid": 1964382, "relation_to_type": "type", "validated": true, "ani": 76.5975, "matched_fragments": 135, "total_fragments": 2013, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_003129525.1", "gtdb_species": "s__Clostridium beijerinckii_D", "ani": 87.0011, "matched_fragments": 993, "total_fragments": 2013, "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_002006345.1", "gtdb_species": "s__Clostridium puniceum", "ani": 83.6463, "matched_fragments": 1010, "total_fragments": 2013, "gtdb_taxonomy": 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