Mutation Profiling of SARS-CoV-2 Sample at Multiple Allele Frequency Thresholds

This dataset contains high-throughput mutation profiling of a SARS-CoV-2 sample: BioSample: SAMN48146492SRA: SRS24854363Isolate name: SARS-CoV-2/human/USA/NJ-GBW-GKISBBBF40282/2025Isolation Source: AN SwabCollecion Date: 15-April-2025Geographical Loction: Newark, New Jersey. USA.Host Info: United Arab Emirates (UAE).Submitter: Ginkgo BioworksVariant Calling and Mutation Profiling conducted by: Tahir HB The Variant Calling and Mutation Profiling analysis was performed using iVar variant calling at three allele frequency thresholds: 1%, 0.5%, and 0.1%. All mutations were matched to known lineage-defining SNPs and annotated based on gene location according to NC_045512.2 Wuhan-Hu-1 reference genome. Files included:- variants_1p.tsv: Mutations called at ≥ 1% AF- variants_0_5p.tsv: Mutations called at ≥ 0.5% AF- variants_0_1p.tsv: Mutations at ≥ 0.1% AF- common_mutations.csv: Mutations found in all three files- unique_mutations_per_pos.csv: Unique mutations per position with AF values- top_common_mutations.csv: Top 30 mutations sorted by AF at 1% level- voc_matched_mutations.csv: Comparison with known VOC markers- mutation_heatmap_common.png: Heatmap of mutation presence across thresholds- mutation_table_by_lineage.csv: Lineage-specific mutation comparison- mutation_presence_heatmap.png: Matches with GISAID profiles The dataset provides insights into mutation patterns, intergenic changes, and conserved lineage markers. This profile shows partial match with Delta variant and stable presence of D614G and T1001I mutations. All files are generated from BAM alignment to NC_045512.2 reference genome and curated for scientific use. Note: Due to file size limitations, larger files such as alignment (BAM/BAI, FASTA/Q etc.) files are not included in this upload. These files are available upon request and can be provided directly by the author if needed for verification or extended analysis.