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    "tally_it",
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        "data.frame"
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        "replicate.y",
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        "REF_COUNT.y",
        "ALT_COUNT.y",
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        "majorcount.y",
        "minorcount.y",
        "majorfreq.y",
        "minorfreq.y",
        "minorfreq",
        "majorfreq",
        "weighted_minorfreq",
        "weighted_majorfreq",
        "SegmentSize",
        "STRAIN",
        "shannon_ntpos",
        "chrom_shannon",
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        "shannon_chrom_perkb",
        "genome_shannon_perkb"
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      "rows": 735,
      "table": true,
      "tojson": true
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      "title": "add_metadata",
      "topics": [
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      "title": "af_distribution",
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      "title": "arrange_data",
      "topics": [
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      "title": "dNdS_segment",
      "topics": [
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    },
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      "topics": [
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    },
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      "title": "filter_variants",
      "topics": [
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      "page": "merge_replicates",
      "title": "merge_replicates",
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      "topics": [
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      "topics": [
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    },
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      "title": "snv_location",
      "topics": [
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        "Compare the similarity between the average allele frequency and the weighted average allele frequency",
        "Filter out variants based on coverage and/or frequency cutoffs",
        "Format SNPeff information",
        "Remove duplicate variants in NS and MP",
        "Add metadata",
        "Step 3: Calculations and Visualization",
        "Plot distribution of all minor variant frequencies",
        "Count number of SNVs",
        "Plot location of SNVs across segments",
        "Plot number of SNVs per sample and per segment",
        "Calculate Transition/Transversion Ratio",
        "Plot TsTv",
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