{ "type": "genome", "identifier": "GCF_003432035.1", "organism": "Lacrimispora amygdalina", "title": "Lacrimispora amygdalina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIR-Institute of Microbial Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003432035.1", "bioproject": "PRJNA224116", "biosample": "SAMN09630405", "wgs_master": "QOHO00000000.1", "refseq_category": "reference genome", "taxid": "253257", "species_taxid": "253257", "organism_name": "Lacrimispora amygdalina", "infraspecific_name": "strain=PI-S10-A1B", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/29", "asm_name": "ASM343203v1", "asm_submitter": "CSIR-Institute of Microbial Technology", "gbrs_paired_asm": "GCA_003432035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/432/035/GCF_003432035.1_ASM343203v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from synonym type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5946122", "genome_size_ungapped": "5946086", "gc_percent": "42.500000", "replicon_count": "0", "scaffold_count": "175", "contig_count": "175", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003432035.1-RS_2024_07_21", "annotation_date": "2024-07-21", "total_gene_count": "5762", "protein_coding_gene_count": "5613", "non_coding_gene_count": "72", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-29", "dateModified": "2018-08-29", "datePublished": "2018-08-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Lacrimispora amygdalina" ], "sample_taxid": [ "253257" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Hyderabad" ], "sample_host_location_id": [], "data_size": "1.691 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)": "5946122", "Number of Sequences": "175", "Longest Sequences (bp)": "199155", "N50 (bp)": "80030", "Gap Ratio (%)": "0.000740", "GCcontent (%)": "42.5", "Number of CDSs": "5673", "Average Protein Length": "312.5", "Coding Ratio (%)": "89.4", "Number of rRNAs": "3", "Number of tRNAs": "65", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lacrimispora aerotolerans", "strain": "strain=DSM 5434", "accession": "GCA_000687555.1", "taxid": 36832, "species_taxid": 36832, "relation_to_type": "type", "validated": true, "ani": 79.5736, "matched_fragments": 546, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lacrimispora sphenoides", "strain": "strain=NCTC507", "accession": "GCA_900461315.1", "taxid": 29370, "species_taxid": 29370, "relation_to_type": "type", "validated": true, "ani": 79.4676, "matched_fragments": 542, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lacrimispora sphenoides", "strain": "strain=ATCC 19403", "accession": "GCA_900105615.1", "taxid": 29370, "species_taxid": 29370, "relation_to_type": "type", "validated": true, "ani": 79.429, "matched_fragments": 543, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lacrimispora celerecrescens", "strain": "strain=18A", "accession": "GCA_002797975.1", "taxid": 29354, "species_taxid": 29354, "relation_to_type": "type", "validated": true, "ani": 79.3597, "matched_fragments": 554, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lacrimispora algidixylanolytica", "strain": "strain=SPL73", "accession": "GCA_003609635.1", "taxid": 94868, "species_taxid": 94868, "relation_to_type": "type", "validated": true, "ani": 78.8906, "matched_fragments": 492, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hungatella hathewayi", "strain": "strain=DSM 13479", "accession": "GCA_025149285.1", "taxid": 154046, "species_taxid": 154046, "relation_to_type": "suspected-type", "validated": true, "ani": 78.3642, "matched_fragments": 260, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hungatella effluvii", "strain": "strain=DSM 24995", "accession": "GCA_003201875.1", "taxid": 1096246, "species_taxid": 1096246, "relation_to_type": "type", "validated": true, "ani": 78.3232, "matched_fragments": 259, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hungatella hathewayi", "strain": "strain=DSM 13479", "accession": "GCA_000160095.1", "taxid": 154046, "species_taxid": 154046, "relation_to_type": "suspected-type", "validated": true, "ani": 78.2824, "matched_fragments": 231, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lachnoclostridium edouardi", "strain": "strain=Marseille-P3397", "accession": "GCA_900240245.1", "taxid": 1926283, "species_taxid": 1926283, "relation_to_type": "type", "validated": true, "ani": 77.4573, "matched_fragments": 109, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia pseudococcoides", "strain": "strain=YL58", "accession": "GCA_001689125.2", "taxid": 1796616, "species_taxid": 1796616, "relation_to_type": "type", "validated": true, "ani": 76.973, "matched_fragments": 64, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia pseudococcoides", "strain": "strain=YL58", "accession": "GCA_002221555.2", "taxid": 1796616, "species_taxid": 1796616, "relation_to_type": "type", "validated": true, "ani": 76.8775, "matched_fragments": 66, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia wexlerae", "strain": "strain=DSM 19850", "accession": "GCA_025148125.1", "taxid": 418240, "species_taxid": 418240, "relation_to_type": "suspected-type", "validated": true, "ani": 76.819, "matched_fragments": 62, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia caecimuris", "strain": "strain=DSM 29492", "accession": "GCA_024622975.1", "taxid": 1796615, "species_taxid": 1796615, "relation_to_type": "type", "validated": true, "ani": 76.6012, "matched_fragments": 54, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003432035.1", "gtdb_species": "s__Lacrimispora indica", "ani": 100.0, "matched_fragments": 1886, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora", "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_013036995.1", "gtdb_species": "s__Lacrimispora xylanolytica_A", "ani": 87.9628, "matched_fragments": 1282, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora", "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_015057705.1", "gtdb_species": "s__Lacrimispora sp015057705", "ani": 87.288, "matched_fragments": 1133, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora", "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_015057715.1", "gtdb_species": "s__Lacrimispora sp015057715", "ani": 87.1118, "matched_fragments": 1142, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora", "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_002934545.1", "gtdb_species": "s__Lacrimispora xylanolytica", "ani": 87.1055, "matched_fragments": 1281, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "98.92", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009712635.1", "gtdb_species": "s__Lacrimispora sp009712635", "ani": 87.0712, "matched_fragments": 1251, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora", "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_015057775.1", "gtdb_species": "s__Lacrimispora sp015057775", "ani": 86.959, "matched_fragments": 978, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora", "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_900205965.1", "gtdb_species": "s__Lacrimispora amygdalina_A", "ani": 86.4229, "matched_fragments": 1227, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora", "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_002797975.1", "gtdb_species": "s__Lacrimispora celerecrescens", "ani": 79.3449, "matched_fragments": 552, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.58", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Lacrimispora", "amygdalina" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }