{ "type": "genome", "identifier": "GCF_004770055.1", "organism": "Leptospira semungkisensis", "title": "Leptospira semungkisensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "INRS-Institut Armand-Frappier", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004770055.1", "bioproject": "PRJNA224116", "biosample": "SAMN10316449", "wgs_master": "RQEP00000000.1", "refseq_category": "reference genome", "taxid": "2484985", "species_taxid": "2484985", "organism_name": "Leptospira semungkisensis", "infraspecific_name": "strain=SSS9", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/10", "asm_name": "ASM477005v1", "asm_submitter": "INRS-Institut Armand-Frappier", "gbrs_paired_asm": "GCA_004770055.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/770/055/GCF_004770055.1_ASM477005v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3944076", "genome_size_ungapped": "3944076", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "26", "contig_count": "26", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004770055.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "3627", "protein_coding_gene_count": "3562", "non_coding_gene_count": "43", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-10", "dateModified": "2019-04-10", "datePublished": "2019-04-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira semungkisensis" ], "sample_taxid": [ "2484985" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Malaysia" ], "sample_host_location_id": [], "data_size": "1.115 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3944076", "Number of Sequences": "26", "Longest Sequences (bp)": "1612815", "N50 (bp)": "832702", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.8", "Number of CDSs": "3548", "Average Protein Length": "335.1", "Coding Ratio (%)": "90.4", "Number of rRNAs": "4", "Number of tRNAs": "37", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira semungkisensis", "strain": "strain=SSS9", "accession": "GCA_004770055.1", "taxid": 2484985, "species_taxid": 2484985, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1305, "total_fragments": 1305, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira langatensis", "strain": "strain=SSW18", "accession": "GCA_004770615.1", "taxid": 2484983, "species_taxid": 2484983, "relation_to_type": "type", "validated": true, "ani": 84.3708, "matched_fragments": 1149, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira saintgironsiae", "strain": "strain=FH4-C-A2", "accession": "GCA_002811765.1", "taxid": 2023183, "species_taxid": 2023183, "relation_to_type": "type", "validated": true, "ani": 79.6271, "matched_fragments": 701, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira selangorensis", "strain": "strain=SSW17", "accession": "GCA_004769405.1", "taxid": 2484982, "species_taxid": 2484982, "relation_to_type": "type", "validated": true, "ani": 79.6252, "matched_fragments": 719, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira venezuelensis", "strain": "strain=CLM-U50", "accession": "GCA_002150035.1", "taxid": 1958811, "species_taxid": 1958811, "relation_to_type": "type", "validated": true, "ani": 79.6215, "matched_fragments": 650, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira licerasiae", "strain": "strain=ATCC BAA-1110", "accession": "GCA_000526875.1", "taxid": 447106, "species_taxid": 447106, "relation_to_type": "type", "validated": true, "ani": 79.5831, "matched_fragments": 701, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira licerasiae", "strain": "strain=VAR 010", "accession": "GCA_000244755.3", "taxid": 447106, "species_taxid": 447106, "relation_to_type": "type", "validated": true, "ani": 79.571, "matched_fragments": 709, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira 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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_004770615.1", "gtdb_species": "s__Leptospira_B langatensis", "ani": 84.3911, "matched_fragments": 1146, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004770895.1", "gtdb_species": "s__Leptospira_B dzoumogneensis", "ani": 79.8897, "matched_fragments": 710, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002811765.1", "gtdb_species": "s__Leptospira_B saintgironsiae", "ani": 79.627, "matched_fragments": 701, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "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_004769405.1", "gtdb_species": "s__Leptospira_B selangorensis", "ani": 79.618, "matched_fragments": 720, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.97", "min_intra_species_ani": "97.97", "mean_intra_species_af": "0.98", 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