{ "type": "genome", "identifier": "GCF_003725735.1", "organism": "Sinomicrobium pectinilyticum", "title": "Sinomicrobium pectinilyticum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Third Institute of Oceanography, State Oceanic Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003725735.1", "bioproject": "PRJNA224116", "biosample": "SAMN10352333", "wgs_master": "RJTM00000000.1", "refseq_category": "reference genome", "taxid": "1084421", "species_taxid": "1084421", "organism_name": "Sinomicrobium pectinilyticum", "infraspecific_name": "strain=5DNS001", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/11/13", "asm_name": "ASM372573v1", "asm_submitter": "Third Institute of Oceanography, State Oceanic Administration", "gbrs_paired_asm": "GCA_003725735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/725/735/GCF_003725735.1_ASM372573v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5648340", "genome_size_ungapped": "5648340", "gc_percent": "44.500000", "replicon_count": "0", "scaffold_count": "235", "contig_count": "235", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003725735.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4612", "protein_coding_gene_count": "4522", "non_coding_gene_count": "45", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-11-13", "dateModified": "2018-11-13", "datePublished": "2018-11-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Sinomicrobium pectinilyticum" ], "sample_taxid": [ "1084421" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Dongying city, Shandong Province, located at the mouth of the Yellow River" ], "sample_host_location_id": [], "data_size": "1.613 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)": "5648340", "Number of Sequences": "235", "Longest Sequences (bp)": "340355", "N50 (bp)": "76253", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.4", "Number of CDSs": "4432", "Average Protein Length": "357.4", "Coding Ratio (%)": "84.1", "Number of rRNAs": "2", "Number of tRNAs": "37", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sinomicrobium pectinilyticum", "strain": "strain=5DNS001", "accession": "GCA_003725735.1", "taxid": 1084421, "species_taxid": 1084421, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1775, "total_fragments": 1782, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sinomicrobium kalidii", "strain": "strain=HD2P242", "accession": "GCA_021183825.1", "taxid": 2900738, "species_taxid": 2900738, "relation_to_type": "type", "validated": true, "ani": 80.0319, "matched_fragments": 780, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinomicrobium oceani", "strain": "strain=CGMCC 1.12145", "accession": "GCA_900119185.1", "taxid": 1150368, "species_taxid": 1150368, "relation_to_type": "type", "validated": true, "ani": 79.8719, "matched_fragments": 688, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinomicrobium weinanense", "strain": "strain=FJxs", "accession": "GCA_018863395.1", "taxid": 2842200, "species_taxid": 2842200, "relation_to_type": "type", "validated": true, "ani": 79.6244, "matched_fragments": 708, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinomicrobium weinanense", "strain": "strain=FJxs", "accession": "GCA_014518365.1", "taxid": 2842200, "species_taxid": 2842200, "relation_to_type": "type", "validated": true, "ani": 79.6004, "matched_fragments": 678, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Robertkochia sediminum", "strain": "strain=1368", "accession": "GCA_016786255.1", "taxid": 2785326, "species_taxid": 2785326, "relation_to_type": "type", "validated": true, "ani": 77.0155, "matched_fragments": 64, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Abyssalbus ytuae", "strain": "strain=MT3330", "accession": "GCA_022807975.1", "taxid": 2926907, "species_taxid": 2926907, "relation_to_type": "type", "validated": true, "ani": 76.9488, "matched_fragments": 78, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003725735.1", "gtdb_species": "s__Sinomicrobium pectinilyticum", "ani": 100.0, "matched_fragments": 1775, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium", "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_900119185.1", "gtdb_species": "s__Sinomicrobium oceani", "ani": 79.8724, "matched_fragments": 689, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium", "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_018863395.1", "gtdb_species": "s__Sinomicrobium sp014518365", "ani": 79.6141, "matched_fragments": 709, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium", "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_010468565.1", "gtdb_species": "s__Muricauda sp010468565", "ani": 79.4522, "matched_fragments": 60, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda", "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_003285545.1", "gtdb_species": "s__Sinomicrobium sp003285545", "ani": 78.3791, "matched_fragments": 451, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium", "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_016786255.1", "gtdb_species": "s__Robertkochia sp016786255", "ani": 77.0155, "matched_fragments": 64, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia", "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_004799345.1", "gtdb_species": "s__Robertkochia marina", "ani": 76.9225, "matched_fragments": 55, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003385855.1", "gtdb_species": "s__Muricauda sp003385855", "ani": 76.5929, "matched_fragments": 53, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.222, "cell_length": 0.633, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 32.5, "optimum_ph": 7.0, "genome_size": 5026272.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Sinomicrobium", "pectinilyticum" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }